Data Import and Processing
Methods
The differential gene expression and gene set analyses were performed in RStudio (Posit team (2023), version 2023.6.2.561, R version 4.3.2 (2023-10-31)).
Differential Transcript Usage Analysis
After detecting differentially expressed genes, differentially expressed isoforms were identified using Differential Transcript Usage (DTU) analysis pipeline using DRIMSeq and DEXSeq libraries. DTU complements DGE as it enables the identification of alternative splicing and isoform switches even if the gene expression does not change between conditions [1, 2]. As for DGE, the aim was to identify differentially expressed isoforms in samples generated over course of the 5 days and to compare the results of the differential gene expression analysis of the Illumina+Salmon data (short read data) with the results of the PacBio+Bambu data (long read data). To do so, in total 8 different count data frames were analyzed. For each of the 4 NDR cutoffs (0.025, 0.05, 0.1, 0.2), there are two different count data frames, one derived from Illumina+Salmon and one derived from PacBio+Bambu. I didn’t change this - I think we can unite DGE and DTU and write that both were conducted - the first two sentences I wrote can just be added after the first sentence of Michel.
The inspiration for this protocol was taken from:
https://ycl6.gitbook.io/guide-to-rna-seq-analysis/differential-expression-analysis/differential-transcript-usage/dtu-using-dexseq
https://www.bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html
References
[1] Marques-Coelho, D., Iohan, L.d.C.C., Melo de Farias, A.R. et al. Differential transcript usage unravels gene expression alterations in Alzheimer’s disease human brains. npj Aging Mech Dis 7, 2 (2021). https://doi.org/10.1038/s41514-020-00052-5
[2] https://www.bioconductor.org/packages/release/workflows/vignettes/rnaseqDTU/inst/doc/rnaseqDTU.html
[3] Anders S, Reyes A, Huber W. Detecting differential usage of exons from RNA-seq data. Genome Res. 2012 Oct;22(10):2008-17. doi: 10.1101/gr.133744.111.
[4] Nowicka M, Robinson MD. DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics. F1000Res. 2016 Jun 13;5:1356. doi: 10.12688/f1000research.8900.2.
Load packages
Load data
The data is loaded from RDS-objects that have been created with the import_processing.qmd file. For each of the 4 NDR cutoffs (0.025, 0.05, 0.1, 0.2), two data frames exist containing the expression data (counts) of the two different technologies used to obtain the data:
Illumina sequencing and Salmon quantification (short read)
PacBio sequencing and Bambu quantification (long read)
In total, this adds up to 8 different data frames. Each of these data frames contains 11 samples, which are replicates from one of five different time points. Each time point has 1-3 replicates.
Load data
df_list_bambu <- readRDS("./bambu.rds")
df_list_salmon <- readRDS("./salmon.rds")
df_list_meta <- readRDS("./meta.rds")
## Salmon
salmon_0.025 <- df_list_salmon$salmon_0.025
salmon_0.05 <- df_list_salmon$salmon_0.05
salmon_0.1 <- df_list_salmon$salmon_0.1
salmon_0.2 <- df_list_salmon$salmon_0.2
## Bambu
bambu_0.025 <- df_list_bambu$bambu_0.025
bambu_0.05 <- df_list_bambu$bambu_0.05
bambu_0.1 <- df_list_bambu$bambu_0.1
bambu_0.2 <- df_list_bambu$bambu_0.2Testing Pipeline
The workflow was taken from
DEXSeq assumes that the feature (transcript) counts follow a negative binomial (NB) distribution and considers them as relative proportions of the group (the gene) using an interaction term in a generalized linear model (GLM) [2, 3]. DRIMSeq assumes that feature proportions follow the Dirichlet distribution (an Dirichlet Multinomial model (MD) for each gene) where the total count for the gene is considered fixed [2, 4].
salmon_0.025
Here, I considered using tximport library for salmon data, however, I realized that it has not been adapted for Bambu data and decided to leave it at counts (the same as in DGE).
library(tximport)
txi <- tximport(c("/home/annatoidze/Documents/ETHZ/STA426/project/data/0.1_salmon_day0-rep1/quant.sf"), type="salmon", txOut=TRUE,
countsFromAbundance="scaledTPM")
cts <- txi$counts
cts <- cts[rowSums(cts) > 0,]
patterns_to_remove <- c("^DQ", "^EF", "^SIRV")
cts <- data.frame(cts)
cts <-
cts[!grepl(paste(patterns_to_remove, collapse = "|"),
rownames(cts)), , drop =F]It is checked how many reads (the range) that mapped to transcriptome using salmon. Also, txdf dataframe is created which maps transcripts to corresponding genes.
range(colSums(salmon_0.025)/1e6) # Between 14.24 and 93.31 million reads mapped to transcriptome based on the replicate[1] 13.65181 90.11048
# Transcript to gene mappings
txdf <- df_list_meta$metagenes_0.025
all(rownames(salmon_0.025) %in% rownames(txdf))[1] TRUE
The samps dataframe relates the sample identifiers to the conditions (in this case, day of the experiment). The cts dataframe corresponds to the counts. In order to run DRIMSeq, a dataframe counts with the gene ID, the feature (transcript) ID, and then columns for each of the samples is built:
DRIMSeq
We create a dmDSdata object with previously generated dataframes.
An object of class dmDSdata
with 61603 genes and 11 samples
* data accessors: counts(), samples()
As the rows of the object are gene oriented, the genes can by checked by rows (sometimes for than one transcript mapped, thus >1 rows shown even if selecting just one):
gene_id feature_id day0.rep1 day0.rep2 day0.rep3 day1.rep1
1 ENSG00000279457.4 BambuTx1 367.532 184.699 410.608 685.231
2 ENSG00000279457.4 ENST00000623083.4 0.000 0.000 0.000 0.000
day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2 day5.rep3
1 436.705 118.02 198.441 867.349 517.19 429.408 492.926
2 0.000 0.00 0.000 0.000 0.00 0.000 0.000
Filtering
The filtering is done using the function dmFilter from DRIMSeq package. n is defined as the minimal number of samples where the genes should be expressed. n.small is the minimal number of samples where the features should be expressed. Both are set to 3, as that is the number of replicates for day 0 and 5. Additional filters are also added: for a transcript to be retained in the dataset, it is required that (1) it has a count of at least 10 in at least n.small samples, (2) it has a relative abundance proportion of at least 0.1 in at least n.small samples, and (3) the total count of the corresponding gene is at least 10 in all n samples.
n <- 3
n.small <- 3
d <- dmFilter(d,
min_samps_feature_expr=n.small, min_feature_expr=10,
min_samps_feature_prop=n.small, min_feature_prop=0.1,
min_samps_gene_expr=n, min_gene_expr=10)
dAn object of class dmDSdata
with 9901 genes and 11 samples
* data accessors: counts(), samples()
It can be seen how many of the remaining genes have N isoforms.
Creating design matrix
The design matrix is created in a way that the first time point, day0, is used as a baseline (intercept of the model).
Precision calculation
dmPrecision is used t estimate the precision by maximum likelihood. It is inversely related to the dispersion in the DM model via following relation: \(dispersion = \frac{1}{1 + precision}\). dmFit is used to fit regression coefficients and estimate feature propotrions for each sample. dmTest is used to perform null hypothesis likelihood ratio testing on day5. plotPrecision is used to plot precision (y-axis) against mean expression (x-axis). In RNA-seq data there is usually a trend of decrease of dispersion (here, increase of precision) with increase of mean expression. This is the trend observed here.
! Using a subset of 0.1 genes to estimate common precision !
! Using common_precision = 21.2862 as prec_init !
! Using loess fit as a shrinkage factor !
user system elapsed
982.117 6.527 991.579
gene_id mean_expression
1 ENSG00000052841.15 4246.4306
2 ENSG00000256591.5 377.4107
3 ENSG00000255471.1 108.7104
4 ENSG00000149328.15 174.1209
5 ENSG00000111186.13 3568.7414
6 ENSG00000111224.14 860.1869
[1] 21.28624
gene_id genewise_precision
1 ENSG00000052841.15 70.800532
2 ENSG00000256591.5 27.737903
3 ENSG00000255471.1 NA
4 ENSG00000149328.15 NA
5 ENSG00000111186.13 5.373339
6 ENSG00000111224.14 11.627499
gene_id feature_id day0.rep1 day0.rep2 day0.rep3 day1.rep1
1 ENSG00000052841.15 BambuTx100 0.1839865 0.1839865 0.1839865 0.1985653
2 ENSG00000052841.15 ENST00000039989.9 0.5718858 0.5718858 0.5718858 0.5620527
3 ENSG00000052841.15 ENST00000299240.10 0.2441277 0.2441277 0.2441277 0.2393820
4 ENSG00000256591.5 BambuTx102 0.3369753 0.3369753 0.3369753 0.4484651
5 ENSG00000256591.5 ENST00000536670.5 0.4133106 0.4133106 0.4133106 0.3925292
6 ENSG00000256591.5 ENST00000541135.5 0.2497141 0.2497141 0.2497141 0.1590057
day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2 day5.rep3
1 0.1146795 0.2187214 0.2187214 0.1995248 0.2203314 0.2203314 0.2203314
2 0.5777165 0.5230367 0.5230367 0.5293489 0.5704172 0.5704172 0.5704172
3 0.3076040 0.2582419 0.2582419 0.2711263 0.2092514 0.2092514 0.2092514
4 0.3755887 0.4164650 0.4164650 0.4029053 0.4589542 0.4589542 0.4589542
5 0.3137564 0.3564449 0.3564449 0.2214526 0.2033833 0.2033833 0.2033833
6 0.3106549 0.2270901 0.2270901 0.3756421 0.3376625 0.3376625 0.3376625
gene_id feature_id X.Intercept. day1 day2
1 ENSG00000052841.15 BambuTx100 -0.2828292 0.095886410 -0.7038428
2 ENSG00000052841.15 ENST00000039989.9 0.8512479 0.002287141 -0.2209780
3 ENSG00000052841.15 ENST00000299240.10 0.0000000 0.000000000 0.0000000
4 ENSG00000256591.5 BambuTx102 0.2996931 0.737197903 -0.1098811
5 ENSG00000256591.5 ENST00000536670.5 0.5038826 0.399788318 -0.4939482
6 ENSG00000256591.5 ENST00000541135.5 0.0000000 0.000000000 0.0000000
day3 day4 day5
1 0.11673115 -0.02381714 0.33442514
2 -0.14549291 -0.18218494 0.15158352
3 0.00000000 0.00000000 0.00000000
4 0.30676255 -0.22962832 0.00721034
5 -0.05304971 -1.03231098 -1.01083724
6 0.00000000 0.00000000 0.00000000
gene_id feature_id X.Intercept. day1 day2
1 ENSG00000052841.15 BambuTx100 -0.2828292 0.095886410 -0.7038428
2 ENSG00000052841.15 ENST00000039989.9 0.8512479 0.002287141 -0.2209780
3 ENSG00000052841.15 ENST00000299240.10 0.0000000 0.000000000 0.0000000
4 ENSG00000256591.5 BambuTx102 0.2996931 0.737197903 -0.1098811
5 ENSG00000256591.5 ENST00000536670.5 0.5038826 0.399788318 -0.4939482
6 ENSG00000256591.5 ENST00000541135.5 0.0000000 0.000000000 0.0000000
day3 day4 day5
1 0.11673115 -0.02381714 0.33442514
2 -0.14549291 -0.18218494 0.15158352
3 0.00000000 0.00000000 0.00000000
4 0.30676255 -0.22962832 0.00721034
5 -0.05304971 -1.03231098 -1.01083724
6 0.00000000 0.00000000 0.00000000
Testing and results
## Fit null model proportions and perform the LR test to detect DTU
d <- dmTest(d, coef="day5")
## Plot the gene-level p-values
plotPValues(d)## Get the gene-level results
## Plot feature proportions for a top DTU gene
res <- DRIMSeq::results(d)
res <- res[order(res$pvalue, decreasing = FALSE), ]
### Get the feature-level results
res.txp <- DRIMSeq::results(d, level="feature")
res.txp <- res.txp[order(res.txp$pvalue, decreasing = FALSE), ]
# Significant gene results
idx <- which(res$adj_pvalue < 0.05)
res[idx,] gene_id lr df pvalue adj_pvalue
7368 ENSG00000112759.19 288.822065 1 8.978826e-65 6.940632e-61
3863 ENSG00000171634.19 256.560124 3 2.493989e-55 9.639269e-52
1659 ENSG00000129422.15 199.630166 3 5.070757e-43 1.306565e-39
4889 ENSG00000107554.17 181.014518 2 4.933975e-40 9.534906e-37
4023 ENSG00000172889.16 157.899284 1 3.255727e-36 5.033354e-33
4219 ENSG00000164587.13 156.329510 2 1.131041e-34 1.457157e-31
8991 ENSG00000151967.18 141.167717 2 2.217276e-31 2.448507e-28
2487 ENSG00000145555.15 138.229088 3 9.105068e-30 8.797772e-27
5509 ENSG00000165629.20 127.371874 1 1.540307e-29 1.322952e-26
1834 ENSG00000026508.21 130.267177 2 5.162284e-29 3.990445e-26
3780 ENSG00000143344.16 118.855868 1 1.126227e-27 7.914302e-25
7381 ENSG00000159658.15 122.200476 2 2.914095e-27 1.877163e-24
5419 ENSG00000186635.15 130.017735 4 3.860201e-27 2.295335e-24
1345 ENSG00000134853.12 113.834644 1 1.416411e-26 7.820610e-24
2803 ENSG00000154380.18 125.840041 4 3.018695e-26 1.555634e-23
5579 ENSG00000093167.18 113.993210 2 1.764773e-25 8.526060e-23
70 ENSG00000153046.18 111.888520 2 5.054946e-25 2.298514e-22
1669 ENSG00000055118.17 114.251722 3 1.334067e-24 5.729078e-22
2833 ENSG00000155307.19 103.970834 2 2.648624e-23 1.077572e-20
6058 ENSG00000125354.24 109.958560 4 7.427273e-23 2.870641e-20
5809 ENSG00000148498.16 112.036216 5 1.520819e-22 5.598064e-20
7142 ENSG00000027869.12 98.636826 2 3.813164e-22 1.339807e-19
1919 ENSG00000115318.12 100.329400 3 1.320284e-21 4.437304e-19
7884 ENSG00000196139.14 99.018780 3 2.526186e-21 8.136425e-19
7584 ENSG00000001497.18 98.031668 3 4.117953e-21 1.273271e-18
7330 ENSG00000024526.17 88.210201 1 5.885560e-21 1.749822e-18
6140 ENSG00000090989.18 91.830058 2 1.146453e-20 3.282253e-18
413 ENSG00000102471.15 91.311997 2 1.485429e-20 4.100844e-18
7594 ENSG00000204301.6 93.569817 3 3.746705e-20 9.986907e-18
5513 ENSG00000065613.15 82.109116 1 1.287773e-19 3.318162e-17
4780 ENSG00000119335.18 83.375116 2 7.858211e-19 1.959483e-16
6867 ENSG00000196549.13 89.788185 4 1.460495e-18 3.528009e-16
7061 ENSG00000143469.20 80.949365 2 2.642827e-18 6.190623e-16
897 ENSG00000076248.11 70.375453 1 4.902620e-17 1.114625e-14
5813 ENSG00000125170.11 74.942531 2 5.326430e-17 1.146762e-14
736 ENSG00000003436.16 78.878403 3 5.340678e-17 1.146762e-14
6795 ENSG00000168918.14 73.440537 2 1.128730e-16 2.358130e-14
5739 ENSG00000069869.17 67.122199 1 2.551887e-16 5.191076e-14
2456 ENSG00000144908.14 71.119619 2 3.602227e-16 7.139798e-14
3120 ENSG00000007392.17 74.460026 3 4.729680e-16 9.140106e-14
3274 ENSG00000163923.10 65.339936 1 6.303099e-16 1.188365e-13
2673 ENSG00000038274.17 64.847789 1 8.091282e-16 1.489181e-13
2151 ENSG00000079102.16 75.194602 4 1.812410e-15 3.258123e-13
5855 ENSG00000185630.19 65.937890 2 4.805838e-15 8.442984e-13
8057 ENSG00000141376.23 64.652763 2 9.137576e-15 1.569632e-12
7754 ENSG00000147044.23 70.220599 4 2.039021e-14 3.426442e-12
2921 ENSG00000187672.14 58.031448 1 2.579608e-14 4.242631e-12
3580 ENSG00000167766.20 63.555153 3 1.021805e-13 1.645532e-11
5426 ENSG00000186439.14 59.349197 2 1.295644e-13 2.043944e-11
6891 ENSG00000138326.21 54.629751 1 1.455160e-13 2.214643e-11
8865 ENSG00000179715.13 59.108767 2 1.461149e-13 2.214643e-11
1310 ENSG00000134001.15 62.550704 3 1.675433e-13 2.490596e-11
5340 ENSG00000185187.13 62.419469 3 1.787237e-13 2.606669e-11
1871 ENSG00000115109.14 58.189938 2 2.313212e-13 3.311320e-11
2453 ENSG00000144857.15 61.156627 3 3.327391e-13 4.676497e-11
2384 ENSG00000143382.16 56.963532 2 4.270966e-13 5.895459e-11
5639 ENSG00000107938.18 56.333866 2 5.851354e-13 7.935257e-11
4875 ENSG00000137868.19 59.667195 3 6.923808e-13 9.227765e-11
8509 ENSG00000225783.9 55.859878 2 7.416204e-13 9.716484e-11
4640 ENSG00000134954.14 55.063671 2 1.104271e-12 1.422670e-10
6489 ENSG00000164209.17 61.224489 4 1.603712e-12 2.032245e-10
300 ENSG00000204314.12 60.301981 4 2.506474e-12 3.125007e-10
4440 ENSG00000060237.19 56.304381 3 3.617327e-12 4.438403e-10
2407 ENSG00000143947.15 48.163361 1 3.921477e-12 4.736409e-10
9094 ENSG00000135253.16 55.619492 3 5.064566e-12 6.022938e-10
5493 ENSG00000187147.18 46.587146 1 8.763320e-12 1.026371e-09
3238 ENSG00000163682.17 57.268406 4 1.086718e-11 1.253781e-09
6781 ENSG00000126883.18 50.337638 2 1.173061e-11 1.333495e-09
2629 ENSG00000014216.16 45.961069 1 1.206264e-11 1.351366e-09
1612 ENSG00000103723.17 53.697596 3 1.301684e-11 1.437431e-09
646 ENSG00000111321.11 45.735987 1 1.353138e-11 1.473206e-09
267 ENSG00000088305.18 45.303951 1 1.687084e-11 1.811272e-09
5915 ENSG00000008130.15 45.014710 1 1.955599e-11 2.070792e-09
3891 ENSG00000169750.9 44.465758 1 2.588451e-11 2.703882e-09
6850 ENSG00000181885.18 44.359875 1 2.732303e-11 2.816093e-09
3935 ENSG00000171992.13 44.260543 1 2.874521e-11 2.906678e-09
8143 ENSG00000109475.17 48.530627 2 2.895397e-11 2.906678e-09
4559 ENSG00000134504.14 51.255793 3 4.315147e-11 4.276421e-09
5158 ENSG00000182287.15 54.261542 4 4.639141e-11 4.539312e-09
411 ENSG00000102316.17 43.286514 1 4.728311e-11 4.545299e-09
5257 ENSG00000128951.14 47.535175 2 4.762862e-11 4.545299e-09
548 ENSG00000106484.16 42.957296 1 5.594786e-11 5.274110e-09
6460 ENSG00000079805.19 50.651255 3 5.804817e-11 5.373357e-09
9113 ENSG00000241472.7 59.443423 6 5.839095e-11 5.373357e-09
2088 ENSG00000122515.16 53.332257 4 7.260991e-11 6.603231e-09
150 ENSG00000031003.11 46.329109 2 8.704860e-11 7.824252e-09
4940 ENSG00000158560.14 46.264526 2 8.990541e-11 7.988147e-09
8562 ENSG00000243004.7 46.207683 2 9.249730e-11 8.125047e-09
4524 ENSG00000100280.17 45.761351 2 1.156243e-10 1.004242e-08
8114 ENSG00000221955.11 45.683201 2 1.202317e-10 1.032657e-08
6721 ENSG00000198561.16 48.947998 3 1.338136e-10 1.136680e-08
3391 ENSG00000165238.17 47.986410 3 2.143709e-10 1.801181e-08
5907 ENSG00000172578.12 44.448684 2 2.228901e-10 1.852625e-08
6569 ENSG00000185963.14 40.185995 1 2.308976e-10 1.894739e-08
6240 ENSG00000168734.14 44.349746 2 2.341936e-10 1.894739e-08
1788 ENSG00000101040.20 47.796198 3 2.353104e-10 1.894739e-08
2879 ENSG00000156482.11 40.085951 1 2.430306e-10 1.936728e-08
7680 ENSG00000204576.12 50.601174 4 2.704333e-10 2.133112e-08
8156 ENSG00000174428.19 47.460486 3 2.773768e-10 2.165780e-08
6107 ENSG00000036054.13 39.731681 1 2.913607e-10 2.252218e-08
3244 ENSG00000163697.17 47.266381 3 3.050458e-10 2.334657e-08
1070 ENSG00000128989.11 39.211646 1 3.802653e-10 2.881814e-08
2118 ENSG00000003147.19 46.675436 3 4.074408e-10 3.057784e-08
6256 ENSG00000143612.21 43.030122 2 4.530307e-10 3.367238e-08
354 ENSG00000075413.19 45.722319 3 6.497309e-10 4.783257e-08
757 ENSG00000115486.13 45.403177 3 7.595846e-10 5.539235e-08
2047 ENSG00000111846.20 41.624648 2 9.147925e-10 6.608734e-08
9115 ENSG00000240225.10 41.522989 2 9.624928e-10 6.888953e-08
4478 ENSG00000168259.17 37.327684 1 9.985697e-10 7.039650e-08
7918 ENSG00000101849.18 41.429603 2 1.008500e-09 7.039650e-08
2515 ENSG00000146263.12 41.424912 2 1.010868e-09 7.039650e-08
4616 ENSG00000137343.18 44.768612 3 1.036194e-09 7.151591e-08
6160 ENSG00000102181.21 37.069016 1 1.140212e-09 7.799855e-08
8796 ENSG00000119559.17 47.158885 4 1.413026e-09 9.581310e-08
8203 ENSG00000196417.13 40.541500 2 1.572263e-09 1.056834e-07
1676 ENSG00000104218.16 40.266300 2 1.804197e-09 1.202280e-07
5515 ENSG00000129353.15 39.734457 2 2.353815e-09 1.537978e-07
5078 ENSG00000101974.15 39.732969 2 2.355567e-09 1.537978e-07
2497 ENSG00000145817.17 39.722735 2 2.367650e-09 1.537978e-07
1206 ENSG00000131089.17 45.964069 4 2.505620e-09 1.614037e-07
4895 ENSG00000071054.17 51.061872 6 2.878373e-09 1.838828e-07
5245 ENSG00000151276.24 35.100401 1 3.131363e-09 1.982148e-07
636 ENSG00000110906.13 35.086375 1 3.154000e-09 1.982148e-07
65 ENSG00000164093.18 45.005544 4 3.965421e-09 2.471992e-07
1573 ENSG00000102804.15 34.523627 1 4.211087e-09 2.604136e-07
6162 ENSG00000142192.21 41.878469 3 4.257587e-09 2.611996e-07
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1877 ENSG00000092445.12 11.866920 2 2.649299e-03 2.383029e-02
1646 ENSG00000037280.16 9.033175 1 2.651235e-03 2.383029e-02
4136 ENSG00000172992.13 11.854659 2 2.665591e-03 2.393150e-02
954 ENSG00000124831.19 14.170725 3 2.681741e-03 2.403563e-02
6325 ENSG00000146828.18 14.167294 3 2.686059e-03 2.403563e-02
8483 ENSG00000232677.10 11.839019 2 2.686518e-03 2.403563e-02
8738 ENSG00000184319.17 16.258064 4 2.691727e-03 2.405439e-02
3856 ENSG00000168916.16 14.156730 3 2.699395e-03 2.406844e-02
8294 ENSG00000214756.8 14.156627 3 2.699526e-03 2.406844e-02
4026 ENSG00000116991.12 14.147647 3 2.710915e-03 2.414214e-02
6455 ENSG00000163946.14 11.805486 2 2.731940e-03 2.430138e-02
726 ENSG00000114857.19 8.967843 1 2.747728e-03 2.439960e-02
963 ENSG00000125375.18 11.792822 2 2.749295e-03 2.439960e-02
4307 ENSG00000168395.16 8.960526 1 2.758755e-03 2.445547e-02
6727 ENSG00000126804.14 11.782071 2 2.764113e-03 2.447491e-02
1678 ENSG00000176406.23 14.080305 3 2.797856e-03 2.474534e-02
3624 ENSG00000168056.18 16.144862 4 2.830815e-03 2.500823e-02
6183 ENSG00000109572.15 14.040921 3 2.849978e-03 2.514878e-02
4816 ENSG00000178209.17 11.713036 2 2.861189e-03 2.521892e-02
4779 ENSG00000177700.6 8.875163 1 2.890764e-03 2.545058e-02
2819 ENSG00000154783.12 11.667508 2 2.927069e-03 2.574089e-02
6894 ENSG00000122390.19 11.646833 2 2.957484e-03 2.596827e-02
8279 ENSG00000253846.3 8.832182 1 2.959644e-03 2.596827e-02
1718 ENSG00000119509.13 11.609131 2 3.013764e-03 2.641315e-02
5411 ENSG00000094631.21 8.789190 1 3.030208e-03 2.652719e-02
8778 ENSG00000196922.11 11.593202 2 3.037862e-03 2.656194e-02
570 ENSG00000107771.17 13.902406 3 3.041050e-03 2.656194e-02
351 ENSG00000100425.19 8.780074 1 3.045389e-03 2.656981e-02
6138 ENSG00000120899.18 8.774755 1 3.054283e-03 2.659262e-02
7872 ENSG00000168994.14 8.774396 1 3.054883e-03 2.659262e-02
6798 ENSG00000140511.12 8.768662 1 3.064501e-03 2.664634e-02
4476 ENSG00000125779.24 15.951659 4 3.084721e-03 2.679202e-02
3793 ENSG00000168672.4 8.715625 1 3.154943e-03 2.737117e-02
6824 ENSG00000196562.15 8.702738 1 3.177324e-03 2.753443e-02
6770 ENSG00000074582.15 13.798481 3 3.192692e-03 2.763663e-02
2935 ENSG00000157764.14 8.690207 1 3.199243e-03 2.763775e-02
2479 ENSG00000145390.12 13.793615 3 3.199972e-03 2.763775e-02
9747 ENSG00000276077.4 11.479882 2 3.214959e-03 2.766373e-02
133 ENSG00000010818.10 8.680831 1 3.215743e-03 2.766373e-02
1848 ENSG00000084234.18 11.479018 2 3.216348e-03 2.766373e-02
5741 ENSG00000261052.6 13.782081 3 3.217296e-03 2.766373e-02
5484 ENSG00000176473.14 11.474136 2 3.224208e-03 2.768946e-02
6620 ENSG00000196843.17 8.672433 1 3.230595e-03 2.768946e-02
7631 ENSG00000095739.11 8.670763 1 3.233557e-03 2.768946e-02
819 ENSG00000116977.19 11.467690 2 3.234617e-03 2.768946e-02
2925 ENSG00000157600.12 11.461930 2 3.243946e-03 2.773861e-02
3416 ENSG00000165689.17 11.450795 2 3.262057e-03 2.786265e-02
5705 ENSG00000153130.18 11.425319 2 3.303874e-03 2.818868e-02
2087 ENSG00000053108.17 13.706207 3 3.333596e-03 2.841092e-02
2123 ENSG00000104691.16 8.591840 1 3.376726e-03 2.874680e-02
6405 ENSG00000179454.14 8.585779 1 3.387984e-03 2.881091e-02
6814 ENSG00000197056.11 11.369113 2 3.398040e-03 2.886467e-02
9022 ENSG00000178971.16 11.338127 2 3.451096e-03 2.928317e-02
5067 ENSG00000185024.18 13.626170 3 3.460793e-03 2.932235e-02
7387 ENSG00000173269.14 8.545749 1 3.463300e-03 2.932235e-02
5712 ENSG00000188529.15 15.685997 4 3.470791e-03 2.935363e-02
121 ENSG00000005882.12 13.616289 3 3.476825e-03 2.937252e-02
2125 ENSG00000087460.29 11.311943 2 3.496574e-03 2.947758e-02
1595 ENSG00000072310.18 11.311764 2 3.496888e-03 2.947758e-02
867 ENSG00000121210.16 11.300270 2 3.517042e-03 2.961518e-02
6672 ENSG00000196730.13 8.513541 1 3.525134e-03 2.965102e-02
1924 ENSG00000058085.15 8.508282 1 3.535336e-03 2.970451e-02
7621 ENSG00000124313.18 13.571201 3 3.550923e-03 2.980308e-02
1142 ENSG00000243156.9 11.274394 2 3.562840e-03 2.987067e-02
5170 ENSG00000185261.15 11.241224 2 3.622423e-03 3.033730e-02
3880 ENSG00000169689.15 11.225331 2 3.651324e-03 3.054625e-02
8908 ENSG00000055163.20 13.475396 3 3.713600e-03 3.103016e-02
704 ENSG00000112983.18 11.188811 2 3.718610e-03 3.103016e-02
4074 ENSG00000113448.20 8.415082 1 3.721211e-03 3.103016e-02
4064 ENSG00000164162.14 13.466036 3 3.729884e-03 3.106499e-02
5183 ENSG00000184809.13 13.464006 3 3.733425e-03 3.106499e-02
6066 ENSG00000106290.16 8.399503 1 3.753237e-03 3.119626e-02
3420 ENSG00000122203.15 8.383951 1 3.785486e-03 3.143051e-02
6488 ENSG00000159199.14 13.423905 3 3.804060e-03 3.155084e-02
8480 ENSG00000231074.10 13.411403 3 3.826350e-03 3.170170e-02
4122 ENSG00000172534.14 8.360169 1 3.835348e-03 3.174223e-02
5795 ENSG00000187764.12 8.356253 1 3.843623e-03 3.177669e-02
2274 ENSG00000140836.17 8.329091 1 3.901517e-03 3.221551e-02
5 ENSG00000111186.13 11.090976 2 3.905036e-03 3.221551e-02
535 ENSG00000106069.24 11.078789 2 3.928906e-03 3.237787e-02
6198 ENSG00000141198.16 13.351862 3 3.934298e-03 3.238778e-02
3159 ENSG00000162714.13 11.063495 2 3.959065e-03 3.255699e-02
5916 ENSG00000184992.13 11.058268 2 3.969425e-03 3.260750e-02
6565 ENSG00000105576.16 8.278176 1 4.012442e-03 3.292588e-02
2924 ENSG00000046889.19 8.255118 1 4.063726e-03 3.325646e-02
5287 ENSG00000183621.15 13.281534 3 4.065689e-03 3.325646e-02
9006 ENSG00000007062.12 11.008248 2 4.069951e-03 3.325646e-02
2211 ENSG00000139372.15 8.250130 1 4.074907e-03 3.325646e-02
3696 ENSG00000186184.20 8.248190 1 4.079265e-03 3.325646e-02
2602 ENSG00000149269.10 11.002692 2 4.081275e-03 3.325646e-02
6136 ENSG00000104497.15 13.272519 3 4.082843e-03 3.325646e-02
3620 ENSG00000168004.10 8.227421 1 4.126211e-03 3.357433e-02
3792 ENSG00000172123.13 8.218042 1 4.147592e-03 3.371281e-02
4303 ENSG00000174238.16 8.197964 1 4.193741e-03 3.405212e-02
6271 ENSG00000122490.19 8.191660 1 4.208340e-03 3.413480e-02
3887 ENSG00000169727.13 10.932308 2 4.227459e-03 3.425394e-02
9221 ENSG00000247708.8 15.236949 4 4.234177e-03 3.427245e-02
2294 ENSG00000141179.14 10.917241 2 4.259428e-03 3.444077e-02
6344 ENSG00000143437.21 10.909576 2 4.275783e-03 3.453689e-02
6920 ENSG00000198901.14 10.880452 2 4.338503e-03 3.500692e-02
690 ENSG00000112559.15 8.116944 1 4.385342e-03 3.534796e-02
6785 ENSG00000174851.16 8.105811 1 4.412357e-03 3.552866e-02
3287 ENSG00000164039.15 8.091437 1 4.447488e-03 3.572260e-02
9133 ENSG00000177679.16 8.091221 1 4.448019e-03 3.572260e-02
7683 ENSG00000204599.15 13.087908 3 4.450305e-03 3.572260e-02
5074 ENSG00000171988.20 8.086540 1 4.459522e-03 3.572641e-02
3794 ENSG00000140987.21 13.082385 3 4.461788e-03 3.572641e-02
5938 ENSG00000188112.9 8.084459 1 4.464646e-03 3.572641e-02
1604 ENSG00000072415.10 13.077686 3 4.471582e-03 3.574491e-02
881 ENSG00000121964.15 13.070855 3 4.485855e-03 3.580381e-02
2464 ENSG00000145029.14 13.069729 3 4.488214e-03 3.580381e-02
2174 ENSG00000114378.17 8.069004 1 4.502885e-03 3.588382e-02
5294 ENSG00000182108.11 8.057843 1 4.530710e-03 3.606837e-02
9811 ENSG00000280623.1 10.784873 2 4.550872e-03 3.619161e-02
785 ENSG00000117385.16 10.762830 2 4.601307e-03 3.654928e-02
8371 ENSG00000108883.13 15.046714 4 4.605304e-03 3.654928e-02
1799 ENSG00000107951.15 8.023518 1 4.617380e-03 3.660754e-02
2941 ENSG00000185585.20 8.016592 1 4.635072e-03 3.671015e-02
6664 ENSG00000164022.18 15.026779 4 4.645998e-03 3.672967e-02
6215 ENSG00000132153.15 8.011922 1 4.647039e-03 3.672967e-02
2089 ENSG00000044090.13 8.006844 1 4.660088e-03 3.679518e-02
1375 ENSG00000115317.12 12.973594 3 4.694058e-03 3.699319e-02
2535 ENSG00000102225.17 12.971615 3 4.698395e-03 3.699319e-02
3709 ENSG00000172071.15 12.971099 3 4.699523e-03 3.699319e-02
6064 ENSG00000221923.9 10.692967 2 4.764876e-03 3.746947e-02
7850 ENSG00000172915.20 7.963442 1 4.773156e-03 3.749644e-02
6687 ENSG00000138119.17 7.961476 1 4.778342e-03 3.749907e-02
8042 ENSG00000146267.12 10.650372 2 4.867445e-03 3.815959e-02
4163 ENSG00000172687.14 10.648122 2 4.872925e-03 3.816384e-02
4004 ENSG00000160072.20 12.875977 3 4.912634e-03 3.843589e-02
7245 ENSG00000116396.15 10.586260 2 5.026004e-03 3.928313e-02
8431 ENSG00000213999.17 10.581106 2 5.038974e-03 3.934472e-02
1405 ENSG00000136014.12 7.854799 1 5.068599e-03 3.953610e-02
8654 ENSG00000104343.21 12.762798 3 5.178685e-03 4.035406e-02
539 ENSG00000106330.12 7.789968 1 5.253713e-03 4.089748e-02
9782 ENSG00000277067.4 10.494714 2 5.261406e-03 4.091616e-02
4538 ENSG00000163867.17 7.777957 1 5.288757e-03 4.108753e-02
9204 ENSG00000245958.7 20.111944 7 5.332895e-03 4.138884e-02
3659 ENSG00000172113.10 12.681159 3 5.379395e-03 4.170119e-02
3667 ENSG00000109919.10 10.448673 2 5.383931e-03 4.170119e-02
3685 ENSG00000075539.15 10.441260 2 5.403923e-03 4.181414e-02
5695 ENSG00000172500.13 7.735853 1 5.413499e-03 4.184635e-02
587 ENSG00000108587.16 7.724820 1 5.446679e-03 4.202589e-02
7328 ENSG00000162623.16 10.424545 2 5.449277e-03 4.202589e-02
6159 ENSG00000112242.16 7.722714 1 5.453036e-03 4.202589e-02
2847 ENSG00000155660.11 7.717976 1 5.467365e-03 4.209435e-02
1458 ENSG00000137177.20 12.640513 3 5.482173e-03 4.216637e-02
6126 ENSG00000127152.18 7.710828 1 5.489058e-03 4.217364e-02
6629 ENSG00000166822.13 7.709193 1 5.494030e-03 4.217364e-02
1534 ENSG00000120802.14 7.686001 1 5.565079e-03 4.267665e-02
6762 ENSG00000025039.15 7.665554 1 5.628498e-03 4.312021e-02
96 ENSG00000254951.7 7.658864 1 5.649406e-03 4.323753e-02
2426 ENSG00000118257.17 10.345339 2 5.669414e-03 4.333125e-02
6141 ENSG00000127870.17 7.651389 1 5.672863e-03 4.333125e-02
409 ENSG00000102265.12 7.645488 1 5.691451e-03 4.343032e-02
3082 ENSG00000161010.16 10.333999 2 5.701652e-03 4.346526e-02
7168 ENSG00000148773.14 7.621042 1 5.769116e-03 4.393622e-02
5089 ENSG00000185842.16 7.610454 1 5.803087e-03 4.415144e-02
8110 ENSG00000187109.15 14.499257 4 5.860852e-03 4.451746e-02
358 ENSG00000100504.17 7.592023 1 5.862713e-03 4.451746e-02
2531 ENSG00000146938.16 10.269116 2 5.889653e-03 4.467814e-02
9170 ENSG00000204152.14 10.252007 2 5.940252e-03 4.501371e-02
1555 ENSG00000158486.14 7.566736 1 5.945537e-03 4.501371e-02
2427 ENSG00000003400.15 7.550992 1 5.997703e-03 4.536423e-02
2160 ENSG00000096746.18 7.548100 1 6.007339e-03 4.537325e-02
5595 ENSG00000145335.17 12.442744 3 6.010634e-03 4.537325e-02
6631 ENSG00000178761.15 12.433638 3 6.036143e-03 4.552135e-02
7947 ENSG00000205763.14 7.531205 1 6.063935e-03 4.568637e-02
5895 ENSG00000104361.10 7.527542 1 6.076274e-03 4.573476e-02
7509 ENSG00000137409.20 7.513633 1 6.123375e-03 4.603776e-02
4732 ENSG00000114503.11 7.512143 1 6.128442e-03 4.603776e-02
3783 ENSG00000100731.16 7.508866 1 6.139602e-03 4.606632e-02
5047 ENSG00000176155.20 12.395495 3 6.144162e-03 4.606632e-02
5269 ENSG00000139117.14 7.451675 1 6.337745e-03 4.747168e-02
3568 ENSG00000109103.12 10.108181 2 6.383171e-03 4.774641e-02
4466 ENSG00000120885.22 10.107051 2 6.386777e-03 4.774641e-02
3311 ENSG00000164168.8 7.434016 1 6.400233e-03 4.780078e-02
6921 ENSG00000198728.11 10.092605 2 6.433075e-03 4.799968e-02
7202 ENSG00000118292.9 7.422544 1 6.441169e-03 4.801373e-02
6839 ENSG00000197102.14 12.274023 3 6.501065e-03 4.838185e-02
4095 ENSG00000119392.16 7.405336 1 6.503071e-03 4.838185e-02
3893 ENSG00000171574.18 7.398558 1 6.527617e-03 4.851777e-02
7738 ENSG00000125864.14 7.389827 1 6.559379e-03 4.870702e-02
8898 ENSG00000223891.7 16.097613 5 6.570840e-03 4.874529e-02
2660 ENSG00000150961.15 7.372551 1 6.622691e-03 4.908284e-02
5129 ENSG00000180881.20 14.217629 4 6.631907e-03 4.910406e-02
1836 ENSG00000113594.10 7.367077 1 6.642881e-03 4.910650e-02
5762 ENSG00000165792.18 12.226909 3 6.644942e-03 4.910650e-02
7400 ENSG00000107263.19 7.364192 1 6.653548e-03 4.912314e-02
5735 ENSG00000213023.11 10.018757 2 6.675051e-03 4.921805e-02
7806 ENSG00000101290.14 7.356185 1 6.683245e-03 4.921805e-02
155 ENSG00000059588.10 7.355577 1 6.685504e-03 4.921805e-02
[1] 1050
gene_id feature_id lr df pvalue
20181 ENSG00000112759.19 ENST00000371755.9 288.822065 1 8.978826e-65
20182 ENSG00000112759.19 ENST00000393844.7 288.822065 1 8.978826e-65
13318 ENSG00000107554.17 ENST00000543621.6 179.903676 1 5.086884e-41
10876 ENSG00000172889.16 ENST00000371698.3 157.899284 1 3.255727e-36
10877 ENSG00000172889.16 ENST00000406555.7 157.899284 1 3.255727e-36
11418 ENSG00000164587.13 ENST00000312037.6 152.797864 1 4.240819e-35
15051 ENSG00000165629.20 ENST00000356708.12 127.371874 1 1.540307e-29
15050 ENSG00000165629.20 ENST00000335698.4 127.371874 1 1.540307e-29
14800 ENSG00000186635.15 ENST00000334211.12 126.273426 1 2.679072e-29
20211 ENSG00000159658.15 ENST00000674435.1 122.906969 1 1.461430e-28
10201 ENSG00000143344.16 ENST00000360851.4 118.855868 1 1.126227e-27
10200 ENSG00000143344.16 ENST00000304685.8 118.855868 1 1.126227e-27
3630 ENSG00000134853.12 ENST00000257290.10 113.834644 1 1.416411e-26
3631 ENSG00000134853.12 ENST00000507536.1 113.834644 1 1.416411e-26
15240 ENSG00000093167.18 ENST00000421276.6 112.120415 1 3.362546e-26
4948 ENSG00000026508.21 ENST00000433892.6 105.723697 1 8.476759e-25
13317 ENSG00000107554.17 ENST00000324109.9 100.531932 1 1.165035e-23
20718 ENSG00000001497.18 ENST00000374811.8 96.889531 1 7.330525e-23
7543 ENSG00000154380.18 ENST00000366843.7 95.611719 1 1.397765e-22
21528 ENSG00000196139.14 ENST00000380554.5 94.460322 1 2.500548e-22
15239 ENSG00000093167.18 ENST00000354379.8 91.533896 1 1.096969e-21
20078 ENSG00000024526.17 ENST00000456315.7 88.210201 1 5.885560e-21
20077 ENSG00000024526.17 ENST00000370966.9 88.210201 1 5.885560e-21
20748 ENSG00000204301.6 ENST00000491215.1 83.198896 1 7.419915e-20
181 ENSG00000153046.18 ENST00000397588.8 82.891759 1 8.667179e-20
15063 ENSG00000065613.15 ENST00000335753.8 82.109116 1 1.287773e-19
15064 ENSG00000065613.15 ENST00000369755.4 82.109116 1 1.287773e-19
16811 ENSG00000090989.18 ENST00000349598.6 77.652634 1 1.228524e-18
4483 ENSG00000129422.15 ENST00000693296.1 76.426957 1 2.285106e-18
5180 ENSG00000115318.12 ENST00000470907.6 75.163547 1 4.332935e-18
13015 ENSG00000119335.18 ENST00000686840.1 74.038529 1 7.660710e-18
19376 ENSG00000143469.20 ENST00000399639.6 73.997259 1 7.822559e-18
13013 ENSG00000119335.18 ENST00000322030.13 72.855704 1 1.394839e-17
2420 ENSG00000076248.11 ENST00000242576.7 70.375453 1 4.902620e-17
2421 ENSG00000076248.11 ENST00000336865.6 70.375453 1 4.902620e-17
15672 ENSG00000069869.17 ENST00000508075.1 67.122199 1 2.551887e-16
15671 ENSG00000069869.17 ENST00000435532.8 67.122199 1 2.551887e-16
16563 ENSG00000125354.24 ENST00000354228.8 65.776564 1 5.050525e-16
8818 ENSG00000163923.10 ENST00000296277.9 65.339936 1 6.303099e-16
8819 ENSG00000163923.10 ENST00000433055.1 65.339936 1 6.303099e-16
7209 ENSG00000038274.17 ENST00000321757.11 64.847789 1 8.091282e-16
7208 ENSG00000038274.17 ENST00000280969.9 64.847789 1 8.091282e-16
4946 ENSG00000026508.21 ENST00000263398.11 63.244676 1 1.825605e-15
7852 ENSG00000187672.14 ENST00000288221.11 58.031448 1 2.579608e-14
7853 ENSG00000187672.14 ENST00000486496.5 58.031448 1 2.579608e-14
14822 ENSG00000186439.14 ENST00000334268.9 57.561431 1 3.275865e-14
15398 ENSG00000107938.18 ENST00000337623.7 56.500519 1 5.618354e-14
5048 ENSG00000115109.14 ENST00000443124.5 56.044447 1 7.085104e-14
9648 ENSG00000167766.20 ENST00000536937.6 55.819684 1 7.943221e-14
6702 ENSG00000145555.15 ENST00000505695.5 55.731543 1 8.307460e-14
23244 ENSG00000225783.9 ENST00000620145.5 55.442961 1 9.621061e-14
18915 ENSG00000138326.21 ENST00000372360.9 54.629751 1 1.455160e-13
18916 ENSG00000138326.21 ENST00000613865.5 54.629751 1 1.455160e-13
19378 ENSG00000143469.20 ENST00000637265.1 53.090028 1 3.186059e-13
15879 ENSG00000125170.11 ENST00000340099.9 52.996673 1 3.341137e-13
8391 ENSG00000007392.17 ENST00000293872.13 51.535622 1 7.030973e-13
12615 ENSG00000134954.14 ENST00000535549.5 50.622131 1 1.119752e-12
18619 ENSG00000126883.18 ENST00000652454.1 50.547783 1 1.162985e-12
6481 ENSG00000143947.15 ENST00000404735.1 48.163361 1 3.921477e-12
6480 ENSG00000143947.15 ENST00000272317.11 48.163361 1 3.921477e-12
3534 ENSG00000134001.15 ENST00000466499.6 47.609077 1 5.202702e-12
20745 ENSG00000204301.6 ENST00000375023.3 47.559731 1 5.335326e-12
5178 ENSG00000115318.12 ENST00000393937.6 47.384876 1 5.833100e-12
1118 ENSG00000102471.15 ENST00000620924.1 46.882350 1 7.537852e-12
15006 ENSG00000187147.18 ENST00000355387.6 46.587146 1 8.763320e-12
15007 ENSG00000187147.18 ENST00000484745.5 46.587146 1 8.763320e-12
21530 ENSG00000196139.14 ENST00000605149.5 46.252863 1 1.039346e-11
7088 ENSG00000014216.16 ENST00000527323.5 45.961069 1 1.206264e-11
7087 ENSG00000014216.16 ENST00000279247.11 45.961069 1 1.206264e-11
12301 ENSG00000100280.17 ENST00000357586.7 45.928564 1 1.226446e-11
1744 ENSG00000111321.11 ENST00000228918.9 45.735987 1 1.353138e-11
1745 ENSG00000111321.11 ENST00000546296.5 45.735987 1 1.353138e-11
17087 ENSG00000168734.14 ENST00000372886.6 45.341265 1 1.655246e-11
722 ENSG00000088305.18 ENST00000328111.6 45.303951 1 1.687084e-11
723 ENSG00000088305.18 ENST00000348286.6 45.303951 1 1.687084e-11
16181 ENSG00000008130.15 ENST00000341426.9 45.014710 1 1.955599e-11
16182 ENSG00000008130.15 ENST00000341991.7 45.014710 1 1.955599e-11
16562 ENSG00000125354.24 ENST00000343984.5 44.730793 1 2.260738e-11
4354 ENSG00000103723.17 ENST00000642989.2 44.470752 1 2.581857e-11
10498 ENSG00000169750.9 ENST00000306897.9 44.465758 1 2.588451e-11
10499 ENSG00000169750.9 ENST00000580965.5 44.465758 1 2.588451e-11
18805 ENSG00000181885.18 ENST00000360325.11 44.359875 1 2.732303e-11
18806 ENSG00000181885.18 ENST00000397317.8 44.359875 1 2.732303e-11
10623 ENSG00000171992.13 ENST00000307662.5 44.260543 1 2.874521e-11
10624 ENSG00000171992.13 ENST00000519664.1 44.260543 1 2.874521e-11
14091 ENSG00000182287.15 ENST00000329235.6 43.683775 1 3.859583e-11
14824 ENSG00000186439.14 ENST00000546248.5 43.519098 1 4.198420e-11
16862 ENSG00000142192.21 ENST00000346798.8 43.375353 1 4.518437e-11
1112 ENSG00000102316.17 ENST00000375068.6 43.286514 1 4.728311e-11
1111 ENSG00000102316.17 ENST00000218439.8 43.286514 1 4.728311e-11
22233 ENSG00000109475.17 ENST00000394665.5 43.241723 1 4.837798e-11
1480 ENSG00000106484.16 ENST00000341441.9 42.957296 1 5.594786e-11
1479 ENSG00000106484.16 ENST00000223215.10 42.957296 1 5.594786e-11
401 ENSG00000031003.11 ENST00000689681.1 42.929937 1 5.673576e-11
17131 ENSG00000143612.21 ENST00000368518.5 42.262961 1 7.978947e-11
13275 ENSG00000137868.19 ENST00000395105.9 41.799678 1 1.011201e-10
23401 ENSG00000243004.7 ENST00000415499.5 41.450226 1 1.209106e-10
21618 ENSG00000101849.18 ENST00000407597.7 41.409390 1 1.234629e-10
8743 ENSG00000163697.17 ENST00000502841.5 41.240503 1 1.346043e-10
16810 ENSG00000090989.18 ENST00000346134.11 41.112373 1 1.437236e-10
16015 ENSG00000173262.12 ENST00000535295.5 41.109507 1 1.439345e-10
6782 ENSG00000146263.12 ENST00000511335.5 40.841761 1 1.650677e-10
10415 ENSG00000171634.19 ENST00000306378.11 40.576600 1 1.890572e-10
5623 ENSG00000122515.16 ENST00000265346.11 40.264643 1 2.217868e-10
18038 ENSG00000185963.14 ENST00000356884.11 40.185995 1 2.308976e-10
18039 ENSG00000185963.14 ENST00000375512.3 40.185995 1 2.308976e-10
7745 ENSG00000156482.11 ENST00000287038.8 40.085951 1 2.430306e-10
7746 ENSG00000156482.11 ENST00000521291.5 40.085951 1 2.430306e-10
12051 ENSG00000060237.19 ENST00000315939.11 39.733789 1 2.910463e-10
16702 ENSG00000036054.13 ENST00000344949.9 39.731681 1 2.913607e-10
16703 ENSG00000036054.13 ENST00000394144.9 39.731681 1 2.913607e-10
8723 ENSG00000163682.17 ENST00000295955.14 39.569967 1 3.165136e-10
2037 ENSG00000115486.13 ENST00000233838.9 39.518364 1 3.249888e-10
7544 ENSG00000154380.18 ENST00000366844.7 39.435728 1 3.390367e-10
180 ENSG00000153046.18 BambuTx53 39.342831 1 3.555560e-10
2899 ENSG00000128989.11 ENST00000566423.5 39.211646 1 3.802653e-10
2898 ENSG00000128989.11 ENST00000249822.9 39.211646 1 3.802653e-10
3293 ENSG00000131477.11 ENST00000253796.10 38.810453 1 4.670203e-10
22386 ENSG00000196417.13 ENST00000396408.8 38.789344 1 4.720981e-10
962 ENSG00000075413.19 ENST00000676938.1 38.490870 1 5.501043e-10
24977 ENSG00000240225.10 ENST00000490123.5 37.996196 1 7.088268e-10
15881 ENSG00000125170.11 ENST00000569548.5 37.951319 1 7.253200e-10
8394 ENSG00000007392.17 ENST00000490762.5 37.828311 1 7.725251e-10
18168 ENSG00000146540.15 ENST00000412051.5 37.762757 1 7.989256e-10
11592 ENSG00000180448.11 ENST00000313093.7 37.528512 1 9.008642e-10
6733 ENSG00000145817.17 ENST00000274496.10 37.352426 1 9.859817e-10
12170 ENSG00000168259.17 ENST00000457167.9 37.327684 1 9.985697e-10
12171 ENSG00000168259.17 ENST00000674214.1 37.327684 1 9.985697e-10
182 ENSG00000153046.18 ENST00000483019.1 37.190051 1 1.071591e-09
18398 ENSG00000205220.12 ENST00000358514.9 37.115589 1 1.113301e-09
22234 ENSG00000109475.17 ENST00000394667.8 37.093885 1 1.125762e-09
16858 ENSG00000102181.21 ENST00000346693.8 37.069016 1 1.140212e-09
16859 ENSG00000102181.21 ENST00000370377.8 37.069016 1 1.140212e-09
20209 ENSG00000159658.15 ENST00000371933.8 36.172560 1 1.805956e-09
20210 ENSG00000159658.15 ENST00000672422.2 36.172560 1 1.805956e-09
23243 ENSG00000225783.9 ENST00000616213.4 35.565384 1 2.466315e-09
17197 ENSG00000117448.14 ENST00000621846.4 35.168334 1 3.024010e-09
14329 ENSG00000151276.24 ENST00000621418.4 35.100401 1 3.131363e-09
14328 ENSG00000151276.24 ENST00000402939.7 35.100401 1 3.131363e-09
1718 ENSG00000110906.13 ENST00000228495.11 35.086375 1 3.154000e-09
1719 ENSG00000110906.13 ENST00000440541.6 35.086375 1 3.154000e-09
15716 ENSG00000164056.11 ENST00000651917.1 34.843307 1 3.573358e-09
19155 ENSG00000169851.15 ENST00000511884.6 34.606333 1 4.035911e-09
4252 ENSG00000102804.15 ENST00000261489.6 34.523627 1 4.211087e-09
4253 ENSG00000102804.15 ENST00000458659.3 34.523627 1 4.211087e-09
12052 ENSG00000060237.19 ENST00000535572.5 34.520106 1 4.218710e-09
17089 ENSG00000168734.14 ENST00000372894.7 34.243134 1 4.863886e-09
3923 ENSG00000136933.17 ENST00000394125.8 34.163768 1 5.066352e-09
22965 ENSG00000242028.8 ENST00000406925.6 34.060451 1 5.342619e-09
22966 ENSG00000242028.8 ENST00000442995.4 34.060451 1 5.342619e-09
15279 ENSG00000158555.15 ENST00000336898.8 33.905258 1 5.786210e-09
15280 ENSG00000158555.15 ENST00000529721.5 33.905258 1 5.786210e-09
17824 ENSG00000164209.17 ENST00000447245.6 33.684947 1 6.480019e-09
15276 ENSG00000100099.21 ENST00000439453.5 33.635339 1 6.647400e-09
15399 ENSG00000107938.18 ENST00000356792.9 33.569616 1 6.875845e-09
3533 ENSG00000134001.15 ENST00000256383.11 33.495321 1 7.143563e-09
13947 ENSG00000184014.9 ENST00000681203.1 33.456301 1 7.288329e-09
18873 ENSG00000111237.19 ENST00000360579.11 33.357973 1 7.666287e-09
22152 ENSG00000221955.11 ENST00000430155.6 33.324264 1 7.800330e-09
11479 ENSG00000137094.16 ENST00000454002.6 33.033262 1 9.059564e-09
11478 ENSG00000137094.16 ENST00000312316.9 33.033262 1 9.059564e-09
18617 ENSG00000126883.18 ENST00000359428.10 32.842708 1 9.992520e-09
15067 ENSG00000129353.15 ENST00000335757.10 32.722822 1 1.062820e-08
6854 ENSG00000133138.20 ENST00000481617.6 32.656920 1 1.099473e-08
6853 ENSG00000133138.20 ENST00000357242.10 32.656920 1 1.099473e-08
12577 ENSG00000166938.13 ENST00000319194.9 32.513380 1 1.183748e-08
16669 ENSG00000124614.16 ENST00000621356.3 32.490224 1 1.197936e-08
16670 ENSG00000124614.16 ENST00000648437.1 32.490224 1 1.197936e-08
19476 ENSG00000152818.19 ENST00000367526.8 32.370288 1 1.274199e-08
19477 ENSG00000152818.19 ENST00000367545.8 32.370288 1 1.274199e-08
8009 ENSG00000127603.32 ENST00000289893.8 32.285753 1 1.330856e-08
6734 ENSG00000145817.17 ENST00000448443.6 31.996010 1 1.544895e-08
166 ENSG00000164093.18 BambuTx40 31.933447 1 1.595462e-08
14124 ENSG00000184489.13 ENST00000520105.5 31.867342 1 1.650693e-08
14361 ENSG00000128951.14 ENST00000331200.8 31.851149 1 1.664512e-08
11295 ENSG00000137478.15 ENST00000311172.11 31.830555 1 1.682254e-08
11296 ENSG00000137478.15 ENST00000409418.9 31.830555 1 1.682254e-08
6799 ENSG00000112531.17 ENST00000361752.8 31.801651 1 1.707476e-08
16852 ENSG00000143369.15 ENST00000369047.9 31.780948 1 1.725774e-08
16853 ENSG00000143369.15 ENST00000470432.5 31.780948 1 1.725774e-08
4087 ENSG00000138162.19 ENST00000369001.5 31.689835 1 1.808663e-08
12613 ENSG00000134954.14 ENST00000392668.8 31.607033 1 1.887448e-08
16062 ENSG00000169398.19 ENST00000519993.5 31.573731 1 1.920094e-08
17613 ENSG00000135316.19 ENST00000355238.11 31.501420 1 1.992945e-08
13872 ENSG00000101974.15 ENST00000361648.6 31.456683 1 2.039395e-08
4947 ENSG00000026508.21 ENST00000425428.6 31.332068 1 2.174579e-08
17553 ENSG00000107518.18 ENST00000609571.5 31.239039 1 2.281320e-08
25614 ENSG00000196951.12 ENST00000608178.6 31.225680 1 2.297072e-08
9455 ENSG00000166847.10 ENST00000300087.7 31.162446 1 2.373129e-08
8365 ENSG00000161835.11 ENST00000293662.9 31.156548 1 2.380350e-08
5512 ENSG00000111846.20 ENST00000379597.7 31.137784 1 2.403471e-08
24735 ENSG00000165821.12 ENST00000614342.1 31.120813 1 2.424577e-08
24734 ENSG00000165821.12 ENST00000537235.2 31.120813 1 2.424577e-08
2290 ENSG00000070087.15 ENST00000239940.12 31.006805 1 2.571254e-08
2291 ENSG00000070087.15 ENST00000452853.6 31.006805 1 2.571254e-08
24078 ENSG00000119559.17 ENST00000586564.5 30.767026 1 2.909398e-08
23875 ENSG00000237515.9 ENST00000558583.3 30.615786 1 3.145242e-08
23874 ENSG00000237515.9 ENST00000423335.2 30.615786 1 3.145242e-08
18090 ENSG00000173209.23 ENST00000394457.7 30.542821 1 3.265781e-08
6574 ENSG00000144677.15 ENST00000443503.6 30.184504 1 3.928357e-08
6573 ENSG00000144677.15 ENST00000273179.10 30.184504 1 3.928357e-08
23806 ENSG00000228624.8 ENST00000517965.1 30.162645 1 3.972884e-08
11420 ENSG00000164587.13 ENST00000521466.5 29.814957 1 4.753108e-08
9272 ENSG00000166130.15 ENST00000299157.5 29.808301 1 4.769455e-08
23448 ENSG00000225953.4 ENST00000666719.2 29.774921 1 4.852286e-08
23449 ENSG00000225953.4 ENST00000668832.1 29.774921 1 4.852286e-08
22798 ENSG00000221978.13 ENST00000400809.8 29.682466 1 5.089308e-08
13725 ENSG00000179222.18 ENST00000326587.12 29.609283 1 5.285123e-08
13726 ENSG00000179222.18 ENST00000375772.7 29.609283 1 5.285123e-08
26433 ENSG00000167680.17 ENST00000586582.6 29.489774 1 5.621250e-08
8487 ENSG00000122417.15 ENST00000317336.11 29.425435 1 5.810995e-08
12544 ENSG00000143624.14 ENST00000481797.5 29.340667 1 6.070820e-08
18400 ENSG00000205220.12 ENST00000570985.1 29.298744 1 6.203588e-08
731 ENSG00000089009.16 ENST00000202773.14 29.276099 1 6.276513e-08
732 ENSG00000089009.16 ENST00000424576.6 29.276099 1 6.276513e-08
6452 ENSG00000143569.19 ENST00000428931.6 29.076844 1 6.956349e-08
3295 ENSG00000131477.11 ENST00000589683.5 28.798788 1 8.030133e-08
2313 ENSG00000108848.16 ENST00000240304.5 28.740621 1 8.274968e-08
20979 ENSG00000204576.12 ENST00000376557.3 28.690783 1 8.490687e-08
7349 ENSG00000152582.14 ENST00000282469.10 28.635998 1 8.734325e-08
7350 ENSG00000152582.14 ENST00000509059.5 28.635998 1 8.734325e-08
18260 ENSG00000182841.13 ENST00000357802.7 28.627788 1 8.771439e-08
13590 ENSG00000100614.18 ENST00000395076.9 28.527590 1 9.237280e-08
4508 ENSG00000055118.17 ENST00000532957.5 28.517113 1 9.287399e-08
2219 ENSG00000119640.9 ENST00000238618.8 28.220132 1 1.082725e-07
24150 ENSG00000133657.17 ENST00000645319.2 28.203129 1 1.092278e-07
7279 ENSG00000109670.16 ENST00000393956.9 28.082342 1 1.162618e-07
18274 ENSG00000138757.15 ENST00000359707.9 28.047101 1 1.183983e-07
24978 ENSG00000240225.10 ENST00000495307.5 27.960949 1 1.237885e-07
24969 ENSG00000241472.7 ENST00000664758.1 27.907739 1 1.272398e-07
10625 ENSG00000166377.21 ENST00000307671.12 27.740964 1 1.386945e-07
7619 ENSG00000155100.11 ENST00000617869.4 27.709900 1 1.409396e-07
12332 ENSG00000140538.16 ENST00000317501.7 27.684417 1 1.428085e-07
14362 ENSG00000128951.14 ENST00000455976.6 27.551354 1 1.529782e-07
17119 ENSG00000072518.22 ENST00000377810.8 27.435005 1 1.624637e-07
8724 ENSG00000163682.17 ENST00000449470.6 27.375194 1 1.675670e-07
15261 ENSG00000075420.13 ENST00000336824.8 27.332545 1 1.713038e-07
21581 ENSG00000205572.10 ENST00000514285.1 27.329787 1 1.715483e-07
8032 ENSG00000159079.19 ENST00000382549.8 27.135112 1 1.897206e-07
2344 ENSG00000114354.15 ENST00000240851.9 27.117341 1 1.914726e-07
22764 ENSG00000215375.6 ENST00000505477.5 27.076234 1 1.955878e-07
13281 ENSG00000156976.17 ENST00000323963.10 27.020991 1 2.012580e-07
4607 ENSG00000109046.15 ENST00000262394.7 27.020415 1 2.013179e-07
8602 ENSG00000163249.13 ENST00000392209.7 27.007262 1 2.026925e-07
3140 ENSG00000203485.14 ENST00000398337.8 26.992762 1 2.042187e-07
25369 ENSG00000245694.11 ENST00000557792.2 26.804625 1 2.250980e-07
18452 ENSG00000198561.16 ENST00000358694.10 26.579797 1 2.528743e-07
5047 ENSG00000115109.14 ENST00000263713.10 26.513593 1 2.616902e-07
6783 ENSG00000146263.12 ENST00000683635.1 26.372293 1 2.815504e-07
8222 ENSG00000160685.14 ENST00000368426.3 26.153456 1 3.153323e-07
22742 ENSG00000185201.18 ENST00000680197.1 26.148658 1 3.161167e-07
3848 ENSG00000136448.13 ENST00000592654.3 26.140295 1 3.174888e-07
8271 ENSG00000160917.15 ENST00000292476.10 26.098849 1 3.243773e-07
8272 ENSG00000160917.15 ENST00000436336.6 26.098849 1 3.243773e-07
17563 ENSG00000133961.21 ENST00000554546.5 26.096322 1 3.248021e-07
12399 ENSG00000134504.14 ENST00000580059.7 26.092895 1 3.253791e-07
16392 ENSG00000158321.18 ENST00000644939.1 25.937885 1 3.525812e-07
3544 ENSG00000134046.12 ENST00000256429.8 25.817022 1 3.753635e-07
9125 ENSG00000165156.15 ENST00000522655.5 25.780525 1 3.825289e-07
5697 ENSG00000003147.19 ENST00000406470.6 25.651694 1 4.089364e-07
22461 ENSG00000250151.9 ENST00000424442.5 25.630270 1 4.135017e-07
399 ENSG00000031003.11 ENST00000033079.7 25.612901 1 4.172404e-07
11593 ENSG00000180448.11 ENST00000543365.5 25.609076 1 4.180684e-07
16849 ENSG00000214063.12 ENST00000527644.2 25.569585 1 4.267128e-07
10692 ENSG00000217128.13 ENST00000510461.6 25.490127 1 4.446525e-07
10691 ENSG00000217128.13 ENST00000307968.11 25.490127 1 4.446525e-07
1987 ENSG00000003436.16 ENST00000421427.5 25.465286 1 4.504146e-07
10763 ENSG00000174099.12 ENST00000355192.8 25.463394 1 4.508566e-07
10762 ENSG00000174099.12 ENST00000308259.10 25.463394 1 4.508566e-07
19626 ENSG00000160710.18 ENST00000529168.2 25.453767 1 4.531119e-07
19625 ENSG00000160710.18 ENST00000368471.8 25.453767 1 4.531119e-07
11519 ENSG00000112763.17 ENST00000312541.10 25.342804 1 4.799395e-07
19950 ENSG00000067208.16 ENST00000370331.5 25.255725 1 5.021031e-07
9127 ENSG00000148187.18 ENST00000344641.8 25.217845 1 5.120621e-07
6175 ENSG00000141068.15 ENST00000644418.1 25.142257 1 5.325305e-07
11318 ENSG00000164114.19 ENST00000650955.1 25.138255 1 5.336368e-07
9124 ENSG00000165156.15 ENST00000395571.8 25.130381 1 5.358201e-07
20982 ENSG00000204576.12 ENST00000481741.5 25.002683 1 5.725058e-07
17823 ENSG00000164209.17 ENST00000355943.8 24.985370 1 5.776699e-07
16926 ENSG00000116698.22 ENST00000347615.6 24.801952 1 6.353311e-07
2794 ENSG00000127511.10 ENST00000248054.10 24.796045 1 6.372811e-07
2795 ENSG00000127511.10 ENST00000596802.5 24.796045 1 6.372811e-07
16352 ENSG00000107758.16 ENST00000394829.6 24.655745 1 6.854012e-07
8662 ENSG00000163513.19 ENST00000359013.4 24.615075 1 7.000197e-07
18655 ENSG00000168918.14 ENST00000445964.6 24.476911 1 7.520568e-07
24288 ENSG00000179715.13 ENST00000432328.2 24.278641 1 8.335831e-07
4319 ENSG00000038532.16 ENST00000261657.5 24.170635 1 8.816641e-07
14750 ENSG00000197928.11 ENST00000598513.6 24.058363 1 9.345945e-07
18453 ENSG00000198561.16 ENST00000529986.5 23.807764 1 1.064522e-06
21924 ENSG00000087152.16 ENST00000389384.8 23.763731 1 1.089156e-06
16063 ENSG00000169398.19 ENST00000521059.5 23.708360 1 1.120945e-06
16024 ENSG00000068366.21 ENST00000672401.1 23.641915 1 1.160324e-06
4720 ENSG00000100813.15 ENST00000605057.6 23.589492 1 1.192369e-06
17919 ENSG00000008838.21 ENST00000394126.5 23.574000 1 1.202008e-06
13871 ENSG00000101974.15 ENST00000327569.7 23.525349 1 1.232788e-06
10376 ENSG00000124134.9 ENST00000306117.5 23.486317 1 1.258053e-06
10377 ENSG00000124134.9 ENST00000537075.3 23.486317 1 1.258053e-06
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4245 ENSG00000092020.11 ENST00000261475.10 16.103608 1 5.996967e-05
20998 ENSG00000106772.19 ENST00000376717.6 16.095843 1 6.021606e-05
22958 ENSG00000185340.15 ENST00000621062.4 16.058362 1 6.141978e-05
14622 ENSG00000182057.5 ENST00000415205.2 16.053835 1 6.156681e-05
17098 ENSG00000132780.17 ENST00000350030.8 16.044535 1 6.186992e-05
5575 ENSG00000138802.11 ENST00000399100.6 16.042367 1 6.194082e-05
12626 ENSG00000141447.19 ENST00000319481.8 16.034973 1 6.218316e-05
19956 ENSG00000075826.17 ENST00000479697.5 15.964630 1 6.453706e-05
16351 ENSG00000107758.16 ENST00000394828.6 15.961719 1 6.463638e-05
17825 ENSG00000164209.17 ENST00000504098.1 15.942406 1 6.529922e-05
10311 ENSG00000112419.15 ENST00000367582.7 15.919676 1 6.608811e-05
10312 ENSG00000112419.15 ENST00000440869.7 15.919676 1 6.608811e-05
5511 ENSG00000111846.20 ENST00000316170.9 15.875095 1 6.766329e-05
10064 ENSG00000171735.19 ENST00000476163.5 15.800694 1 7.037669e-05
1672 ENSG00000109944.11 ENST00000307257.10 15.800576 1 7.038107e-05
16017 ENSG00000173262.12 ENST00000542546.5 15.790480 1 7.075764e-05
4529 ENSG00000104218.16 ENST00000678645.1 15.783231 1 7.102926e-05
18884 ENSG00000134884.15 ENST00000400198.8 15.770552 1 7.150686e-05
18885 ENSG00000134884.15 ENST00000472226.2 15.770552 1 7.150686e-05
8393 ENSG00000007392.17 ENST00000426094.5 15.743376 1 7.254150e-05
25613 ENSG00000196951.12 ENST00000512692.7 15.740064 1 7.266860e-05
15273 ENSG00000100099.21 ENST00000336873.9 15.734857 1 7.286894e-05
10785 ENSG00000164305.19 ENST00000523916.5 15.714527 1 7.365631e-05
10784 ENSG00000164305.19 ENST00000308394.9 15.714527 1 7.365631e-05
4352 ENSG00000103723.17 ENST00000535513.2 15.646449 1 7.635582e-05
23104 ENSG00000234741.9 ENST00000650796.1 15.638554 1 7.667524e-05
23006 ENSG00000071189.21 ENST00000428135.7 15.625084 1 7.722335e-05
5850 ENSG00000107864.15 ENST00000614585.4 15.612137 1 7.775392e-05
223 ENSG00000253507.6 BambuTx85 15.598690 1 7.830884e-05
23639 ENSG00000099810.21 ENST00000580900.5 15.572275 1 7.941050e-05
17360 ENSG00000170456.16 ENST00000389082.10 15.568963 1 7.954975e-05
17361 ENSG00000170456.16 ENST00000546299.1 15.568963 1 7.954975e-05
152 ENSG00000127483.19 BambuTx3 15.563742 1 7.976970e-05
13498 ENSG00000137473.19 ENST00000504425.5 15.558157 1 8.000572e-05
13497 ENSG00000137473.19 ENST00000325106.9 15.558157 1 8.000572e-05
15702 ENSG00000165246.15 ENST00000355905.6 15.545667 1 8.053601e-05
18953 ENSG00000197879.17 ENST00000648651.1 15.528543 1 8.126885e-05
3254 ENSG00000131051.24 ENST00000361162.10 15.525852 1 8.138461e-05
6450 ENSG00000143569.19 ENST00000271877.11 15.519971 1 8.163817e-05
16972 ENSG00000119139.21 ENST00000377245.9 15.494979 1 8.272470e-05
3457 ENSG00000141219.16 ENST00000359042.6 15.494435 1 8.274853e-05
187 ENSG00000124523.17 ENST00000379250.10 15.490270 1 8.293107e-05
13767 ENSG00000171606.18 ENST00000610905.4 15.440720 1 8.513397e-05
156 ENSG00000265992.1 ENST00000583516.1 15.438476 1 8.523509e-05
155 ENSG00000265992.1 BambuTx31 15.438476 1 8.523509e-05
1309 ENSG00000104852.15 ENST00000544278.2 15.431435 1 8.555326e-05
9296 ENSG00000166169.17 ENST00000370169.5 15.428595 1 8.568193e-05
11259 ENSG00000178821.13 ENST00000378602.3 15.420665 1 8.604223e-05
4747 ENSG00000035862.12 ENST00000585421.5 15.408456 1 8.659988e-05
4746 ENSG00000035862.12 ENST00000262768.11 15.408456 1 8.659988e-05
4054 ENSG00000137942.18 ENST00000260506.12 15.402739 1 8.686231e-05
4055 ENSG00000137942.18 ENST00000370253.6 15.402739 1 8.686231e-05
24631 ENSG00000151967.18 ENST00000482885.1 15.402441 1 8.687598e-05
6703 ENSG00000145555.15 ENST00000513610.6 15.401678 1 8.691107e-05
17968 ENSG00000105220.17 ENST00000588991.7 15.382983 1 8.777524e-05
4122 ENSG00000171681.13 ENST00000540793.5 15.350687 1 8.928847e-05
12043 ENSG00000114779.20 ENST00000361143.10 15.350060 1 8.931807e-05
18484 ENSG00000077458.13 ENST00000398187.6 15.301179 1 9.165928e-05
22617 ENSG00000104885.19 ENST00000398665.8 15.298171 1 9.180533e-05
22618 ENSG00000104885.19 ENST00000686010.1 15.298171 1 9.180533e-05
22886 ENSG00000049323.16 ENST00000407925.5 15.294656 1 9.197637e-05
17537 ENSG00000197586.13 ENST00000354989.9 15.271134 1 9.312887e-05
26301 ENSG00000284634.1 ENST00000642112.1 15.234698 1 9.494288e-05
11745 ENSG00000138668.19 ENST00000352301.8 15.229737 1 9.519261e-05
3589 ENSG00000134324.12 ENST00000256720.6 15.228031 1 9.527865e-05
3590 ENSG00000134324.12 ENST00000674199.1 15.228031 1 9.527865e-05
20394 ENSG00000102384.14 ENST00000684367.1 15.222889 1 9.553840e-05
18375 ENSG00000197448.14 ENST00000358406.10 15.219163 1 9.572709e-05
10491 ENSG00000172239.14 ENST00000306846.8 15.208433 1 9.627253e-05
10492 ENSG00000172239.14 ENST00000436644.6 15.208433 1 9.627253e-05
1602 ENSG00000108773.11 ENST00000225916.10 15.188967 1 9.727006e-05
1603 ENSG00000108773.11 ENST00000465682.5 15.188967 1 9.727006e-05
13276 ENSG00000137868.19 ENST00000432245.6 15.174450 1 9.802079e-05
24063 ENSG00000170381.14 ENST00000643230.2 15.129226 1 1.003969e-04
7080 ENSG00000125991.21 ENST00000496172.5 15.123862 1 1.006826e-04
7079 ENSG00000125991.21 ENST00000348547.7 15.123862 1 1.006826e-04
9683 ENSG00000167703.15 ENST00000301335.10 15.098556 1 1.020413e-04
5937 ENSG00000072041.18 ENST00000680379.1 15.086160 1 1.027136e-04
13282 ENSG00000156976.17 ENST00000425053.5 15.072155 1 1.034785e-04
19729 ENSG00000151923.18 ENST00000436547.7 15.071618 1 1.035080e-04
10732 ENSG00000175309.15 ENST00000476170.2 15.058019 1 1.042564e-04
16830 ENSG00000065534.20 ENST00000685953.1 15.042233 1 1.051320e-04
23168 ENSG00000212719.14 ENST00000653508.1 15.039154 1 1.053037e-04
39 ENSG00000140750.17 BambuTx130 15.004153 1 1.072748e-04
340 ENSG00000010219.14 ENST00000543431.6 14.984174 1 1.084166e-04
9238 ENSG00000165916.9 ENST00000602866.5 14.955770 1 1.100610e-04
17940 ENSG00000073921.18 ENST00000526033.5 14.941124 1 1.109187e-04
2314 ENSG00000108848.16 ENST00000393227.6 14.923727 1 1.119462e-04
10758 ENSG00000174136.13 ENST00000308234.11 14.916761 1 1.123603e-04
10759 ENSG00000174136.13 ENST00000513185.3 14.916761 1 1.123603e-04
4085 ENSG00000138162.19 ENST00000360561.7 14.900772 1 1.133166e-04
8894 ENSG00000164100.9 ENST00000296499.6 14.889556 1 1.139923e-04
8895 ENSG00000164100.9 ENST00000394488.2 14.889556 1 1.139923e-04
24016 ENSG00000237441.10 ENST00000437840.6 14.877601 1 1.147171e-04
7987 ENSG00000158604.15 ENST00000457408.7 14.867861 1 1.153109e-04
7988 ENSG00000158604.15 ENST00000481238.1 14.867861 1 1.153109e-04
7779 ENSG00000156925.12 ENST00000287538.10 14.836308 1 1.172562e-04
7780 ENSG00000156925.12 ENST00000370606.3 14.836308 1 1.172562e-04
18507 ENSG00000165280.18 ENST00000358901.11 14.827566 1 1.178009e-04
18508 ENSG00000165280.18 ENST00000679204.2 14.827566 1 1.178009e-04
15396 ENSG00000122565.19 ENST00000337620.8 14.822205 1 1.181363e-04
15397 ENSG00000122565.19 ENST00000396386.7 14.822205 1 1.181363e-04
24152 ENSG00000227398.5 ENST00000429315.3 14.813219 1 1.187006e-04
17099 ENSG00000132780.17 ENST00000351223.7 14.812291 1 1.187590e-04
23809 ENSG00000228624.8 ENST00000691803.1 14.777141 1 1.209934e-04
2227 ENSG00000119673.16 ENST00000238651.10 14.772459 1 1.212941e-04
24834 ENSG00000149260.18 ENST00000456580.6 14.759243 1 1.221473e-04
24835 ENSG00000149260.18 ENST00000648180.1 14.759243 1 1.221473e-04
14441 ENSG00000182541.18 ENST00000333611.8 14.758908 1 1.221689e-04
22356 ENSG00000185219.18 ENST00000396077.8 14.731705 1 1.239444e-04
22357 ENSG00000185219.18 ENST00000425708.6 14.731705 1 1.239444e-04
10663 ENSG00000100461.18 ENST00000399922.6 14.692208 1 1.265685e-04
4076 ENSG00000138078.16 ENST00000409936.5 14.656113 1 1.290156e-04
7626 ENSG00000155307.19 ENST00000647101.1 14.588936 1 1.336972e-04
23403 ENSG00000243004.7 ENST00000457921.6 14.581894 1 1.341978e-04
1812 ENSG00000010810.17 ENST00000368678.8 14.549050 1 1.365575e-04
10522 ENSG00000170234.13 ENST00000307063.9 14.530848 1 1.378832e-04
10523 ENSG00000170234.13 ENST00000456329.7 14.530848 1 1.378832e-04
5635 ENSG00000099250.18 ENST00000374822.8 14.510091 1 1.394108e-04
20562 ENSG00000180198.17 ENST00000683442.1 14.509623 1 1.394454e-04
11425 ENSG00000175216.15 ENST00000529230.6 14.488175 1 1.410422e-04
5538 ENSG00000113318.11 ENST00000265081.7 14.479260 1 1.417112e-04
5539 ENSG00000113318.11 ENST00000658259.1 14.479260 1 1.417112e-04
22393 ENSG00000100167.21 ENST00000644076.2 14.471552 1 1.422924e-04
15178 ENSG00000143702.16 ENST00000366542.6 14.466796 1 1.426521e-04
10808 ENSG00000048649.14 ENST00000308488.11 14.464381 1 1.428351e-04
20190 ENSG00000160345.13 ENST00000371789.7 14.427023 1 1.456966e-04
20191 ENSG00000160345.13 ENST00000429260.7 14.427023 1 1.456966e-04
4452 ENSG00000119707.14 ENST00000532683.5 14.415387 1 1.465996e-04
739 ENSG00000249115.9 ENST00000203166.10 14.394473 1 1.482368e-04
740 ENSG00000249115.9 ENST00000585968.5 14.394473 1 1.482368e-04
11251 ENSG00000115677.18 ENST00000391976.6 14.377098 1 1.496109e-04
11250 ENSG00000115677.18 ENST00000310931.10 14.377098 1 1.496109e-04
12925 ENSG00000177311.12 ENST00000321464.7 14.373924 1 1.498633e-04
12926 ENSG00000177311.12 ENST00000637056.1 14.373924 1 1.498633e-04
26904 ENSG00000283196.2 ENST00000636531.1 14.319801 1 1.542340e-04
13878 ENSG00000198040.11 ENST00000543758.5 14.315920 1 1.545523e-04
13877 ENSG00000198040.11 ENST00000539354.6 14.315920 1 1.545523e-04
10904 ENSG00000002330.14 ENST00000309032.8 14.274407 1 1.579986e-04
10905 ENSG00000002330.14 ENST00000394532.7 14.274407 1 1.579986e-04
15849 ENSG00000001631.17 ENST00000692807.1 14.272384 1 1.581685e-04
18635 ENSG00000169359.16 ENST00000643144.2 14.270509 1 1.583262e-04
9043 ENSG00000164830.19 ENST00000297447.10 14.265947 1 1.587103e-04
2345 ENSG00000114354.15 ENST00000490574.6 14.251697 1 1.599166e-04
13062 ENSG00000136709.12 ENST00000322313.9 14.220842 1 1.625601e-04
13063 ENSG00000136709.12 ENST00000409658.7 14.220842 1 1.625601e-04
10887 ENSG00000116991.12 ENST00000675407.1 14.192806 1 1.650002e-04
11315 ENSG00000164114.19 ENST00000311277.9 14.167602 1 1.672253e-04
13117 ENSG00000117335.20 ENST00000367042.6 14.165713 1 1.673932e-04
11705 ENSG00000166444.19 ENST00000532162.5 14.146469 1 1.691142e-04
18793 ENSG00000150636.17 ENST00000580292.2 14.139314 1 1.697587e-04
9763 ENSG00000085733.16 ENST00000301843.13 14.138665 1 1.698172e-04
9764 ENSG00000085733.16 ENST00000346329.7 14.138665 1 1.698172e-04
7610 ENSG00000154917.11 ENST00000285208.9 14.110615 1 1.723683e-04
7611 ENSG00000154917.11 ENST00000486858.5 14.110615 1 1.723683e-04
8750 ENSG00000163704.12 ENST00000412055.6 14.097740 1 1.735522e-04
8749 ENSG00000163704.12 ENST00000411976.2 14.097740 1 1.735522e-04
20633 ENSG00000158006.14 ENST00000374282.8 14.088552 1 1.744020e-04
20634 ENSG00000158006.14 ENST00000374284.5 14.088552 1 1.744020e-04
12582 ENSG00000107186.17 ENST00000536827.5 14.076288 1 1.755429e-04
12906 ENSG00000013441.17 ENST00000432425.5 14.073354 1 1.758170e-04
22864 ENSG00000108883.13 ENST00000591382.5 14.049818 1 1.780311e-04
20671 ENSG00000112514.18 ENST00000607266.5 14.030019 1 1.799153e-04
17499 ENSG00000004455.17 ENST00000373449.7 14.022249 1 1.806602e-04
12542 ENSG00000143624.14 ENST00000435409.6 14.013069 1 1.815444e-04
15494 ENSG00000068305.18 ENST00000557942.6 13.957954 1 1.869450e-04
24421 ENSG00000169855.21 ENST00000618846.4 13.943882 1 1.883496e-04
18958 ENSG00000158691.15 ENST00000684592.1 13.943579 1 1.883800e-04
10180 ENSG00000168958.20 ENST00000304593.14 13.884840 1 1.943599e-04
8603 ENSG00000163281.12 ENST00000295448.8 13.875218 1 1.953575e-04
2060 ENSG00000115806.13 ENST00000234160.5 13.867225 1 1.961902e-04
2061 ENSG00000115806.13 ENST00000442798.5 13.867225 1 1.961902e-04
22388 ENSG00000196417.13 ENST00000594030.2 13.866702 1 1.962448e-04
25975 ENSG00000257621.9 ENST00000554360.5 13.852010 1 1.977851e-04
21771 ENSG00000155269.12 ENST00000382487.5 13.851950 1 1.977914e-04
21772 ENSG00000155269.12 ENST00000513120.2 13.851950 1 1.977914e-04
5384 ENSG00000108306.13 ENST00000394294.7 13.843261 1 1.987081e-04
10398 ENSG00000168916.16 ENST00000504926.5 13.821237 1 2.010509e-04
17920 ENSG00000008838.21 ENST00000394128.7 13.814373 1 2.017867e-04
27032 ENSG00000288663.1 ENST00000679196.1 13.798452 1 2.035039e-04
14880 ENSG00000109184.15 ENST00000477560.5 13.781079 1 2.053944e-04
5493 ENSG00000114107.9 ENST00000481834.5 13.766597 1 2.069839e-04
22385 ENSG00000187735.15 ENST00000640382.1 13.750788 1 2.087332e-04
18189 ENSG00000112200.17 ENST00000370708.8 13.726572 1 2.114417e-04
18791 ENSG00000150636.17 ENST00000360242.9 13.701260 1 2.143106e-04
16110 ENSG00000055732.13 ENST00000370589.7 13.681897 1 2.165318e-04
12062 ENSG00000107957.17 ENST00000692756.1 13.637038 1 2.217670e-04
3514 ENSG00000133812.18 ENST00000256190.13 13.627921 1 2.228465e-04
3515 ENSG00000133812.18 ENST00000689128.1 13.627921 1 2.228465e-04
16660 ENSG00000127616.20 ENST00000647230.1 13.591019 1 2.272702e-04
13782 ENSG00000157216.16 ENST00000371319.8 13.568103 1 2.300617e-04
16543 ENSG00000129691.16 ENST00000428278.6 13.567275 1 2.301632e-04
16542 ENSG00000129691.16 ENST00000343823.11 13.567275 1 2.301632e-04
6678 ENSG00000145375.9 ENST00000422835.2 13.560654 1 2.309766e-04
4717 ENSG00000100813.15 ENST00000357481.6 13.556398 1 2.315009e-04
6174 ENSG00000141068.15 ENST00000398988.7 13.551918 1 2.320542e-04
24726 ENSG00000223756.8 ENST00000533775.6 13.550712 1 2.322033e-04
23919 ENSG00000184319.17 ENST00000686213.1 13.533141 1 2.343874e-04
5198 ENSG00000082258.13 ENST00000419781.5 13.516833 1 2.364331e-04
9044 ENSG00000164830.19 ENST00000312046.10 13.515300 1 2.366263e-04
1507 ENSG00000106692.15 ENST00000223528.6 13.509885 1 2.373101e-04
2784 ENSG00000130803.15 ENST00000247956.11 13.488843 1 2.399862e-04
2785 ENSG00000130803.15 ENST00000360385.7 13.488843 1 2.399862e-04
17591 ENSG00000133104.14 ENST00000438666.7 13.466071 1 2.429165e-04
10662 ENSG00000100461.18 ENST00000359890.8 13.462869 1 2.433314e-04
9539 ENSG00000167191.12 ENST00000569479.5 13.445935 1 2.455376e-04
19265 ENSG00000160691.19 ENST00000368445.9 13.440123 1 2.462995e-04
2924 ENSG00000129255.16 ENST00000250124.11 13.430351 1 2.475858e-04
2925 ENSG00000129255.16 ENST00000574558.1 13.430351 1 2.475858e-04
18068 ENSG00000099246.18 ENST00000682852.1 13.424767 1 2.483238e-04
17840 ENSG00000234719.9 ENST00000540412.1 13.411046 1 2.501468e-04
17987 ENSG00000160752.15 ENST00000447866.5 13.407165 1 2.506650e-04
8607 ENSG00000152795.18 ENST00000602300.5 13.403984 1 2.510904e-04
8606 ENSG00000152795.18 ENST00000507721.5 13.403984 1 2.510904e-04
22941 ENSG00000164199.18 ENST00000425867.3 13.400078 1 2.516138e-04
10300 ENSG00000187741.15 ENST00000568369.5 13.395417 1 2.522398e-04
5886 ENSG00000087470.19 ENST00000452533.6 13.352143 1 2.581275e-04
2824 ENSG00000127824.15 ENST00000248437.9 13.325499 1 2.618212e-04
2825 ENSG00000127824.15 ENST00000498660.1 13.325499 1 2.618212e-04
7740 ENSG00000156453.14 ENST00000357517.6 13.311786 1 2.637430e-04
147 ENSG00000131375.10 BambuTx28 13.290845 1 2.667052e-04
148 ENSG00000131375.10 ENST00000253693.7 13.290845 1 2.667052e-04
17075 ENSG00000166833.23 ENST00000396085.6 13.290039 1 2.668199e-04
14580 ENSG00000182718.18 ENST00000451270.7 13.285965 1 2.674004e-04
14579 ENSG00000182718.18 ENST00000421017.6 13.285965 1 2.674004e-04
2517 ENSG00000124140.15 ENST00000413737.2 13.283153 1 2.678017e-04
7973 ENSG00000005187.12 ENST00000614721.1 13.268327 1 2.699279e-04
3573 ENSG00000134285.11 ENST00000550765.6 13.248054 1 2.728631e-04
13438 ENSG00000116191.19 ENST00000367634.7 13.245435 1 2.732445e-04
13439 ENSG00000116191.19 ENST00000367635.8 13.245435 1 2.732445e-04
17014 ENSG00000100241.22 ENST00000684986.1 13.205534 1 2.791236e-04
16925 ENSG00000109572.15 ENST00000613795.4 13.185420 1 2.821355e-04
10469 ENSG00000144354.14 ENST00000306721.8 13.153831 1 2.869320e-04
10753 ENSG00000174628.16 ENST00000568300.6 13.148699 1 2.877190e-04
22005 ENSG00000212123.4 ENST00000390672.2 13.132981 1 2.901428e-04
22006 ENSG00000212123.4 ENST00000419421.3 13.132981 1 2.901428e-04
17328 ENSG00000146828.18 ENST00000354161.8 13.117096 1 2.926133e-04
21264 ENSG00000138050.15 ENST00000505747.6 13.109993 1 2.937248e-04
22140 ENSG00000187109.15 ENST00000548044.5 13.109677 1 2.937743e-04
15177 ENSG00000143702.16 ENST00000336415.8 13.109519 1 2.937991e-04
16726 ENSG00000181852.18 ENST00000615206.4 13.096915 1 2.957824e-04
23402 ENSG00000243004.7 ENST00000449573.5 13.080772 1 2.983425e-04
21230 ENSG00000182220.15 ENST00000638153.1 13.060869 1 3.015295e-04
13279 ENSG00000168952.16 ENST00000396700.5 13.047209 1 3.037367e-04
25578 ENSG00000281501.1 ENST00000507794.2 13.032966 1 3.060554e-04
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18998 ENSG00000198728.11 ENST00000673968.1 9.279293 1 2.317588e-03
10244 ENSG00000106400.12 ENST00000305105.3 9.279005 1 2.317953e-03
12905 ENSG00000013441.17 ENST00000321356.9 9.272349 1 2.326391e-03
19037 ENSG00000110002.16 ENST00000361352.9 9.272100 1 2.326707e-03
17854 ENSG00000019144.20 ENST00000534140.2 9.270694 1 2.328495e-03
13263 ENSG00000173818.17 ENST00000518137.6 9.266099 1 2.334344e-03
8480 ENSG00000162642.14 ENST00000294661.8 9.263347 1 2.337854e-03
1534 ENSG00000107771.17 ENST00000224756.12 9.262991 1 2.338308e-03
3507 ENSG00000133731.10 ENST00000449740.6 9.260094 1 2.342010e-03
45 ENSG00000103121.9 BambuTx132 9.246992 1 2.358826e-03
21735 ENSG00000104723.21 ENST00000382020.8 9.242699 1 2.364362e-03
7337 ENSG00000251201.8 ENST00000282382.8 9.226145 1 2.385835e-03
7338 ENSG00000251201.8 ENST00000333314.3 9.226145 1 2.385835e-03
6824 ENSG00000146938.16 ENST00000381095.8 9.224899 1 2.387459e-03
7785 ENSG00000156931.16 ENST00000436792.6 9.224617 1 2.387826e-03
7784 ENSG00000156931.16 ENST00000287546.8 9.224617 1 2.387826e-03
16723 ENSG00000181852.18 ENST00000345093.9 9.223972 1 2.388667e-03
20902 ENSG00000263020.6 ENST00000375880.6 9.219288 1 2.394786e-03
6449 ENSG00000143554.14 ENST00000624995.4 9.218864 1 2.395342e-03
15573 ENSG00000153130.18 ENST00000338517.8 9.218305 1 2.396073e-03
4128 ENSG00000070961.16 ENST00000428670.8 9.211928 1 2.404433e-03
2091 ENSG00000116670.15 ENST00000376667.7 9.207401 1 2.410387e-03
2092 ENSG00000116670.15 ENST00000376692.9 9.207401 1 2.410387e-03
22018 ENSG00000178935.5 ENST00000596248.1 9.200326 1 2.419721e-03
22017 ENSG00000178935.5 ENST00000391701.1 9.200326 1 2.419721e-03
12628 ENSG00000141447.19 ENST00000399443.7 9.193500 1 2.428760e-03
26393 ENSG00000267383.8 ENST00000592022.1 9.193218 1 2.429134e-03
26392 ENSG00000267383.8 ENST00000585816.1 9.193218 1 2.429134e-03
9952 ENSG00000132535.22 ENST00000489885.1 9.191849 1 2.430952e-03
1008 ENSG00000100836.11 ENST00000397276.6 9.178477 1 2.448778e-03
1007 ENSG00000100836.11 ENST00000216727.9 9.178477 1 2.448778e-03
17812 ENSG00000197321.16 ENST00000375400.7 9.170876 1 2.458968e-03
9129 ENSG00000148187.18 ENST00000373729.5 9.166133 1 2.465349e-03
12302 ENSG00000100280.17 ENST00000405198.6 9.157008 1 2.477674e-03
12303 ENSG00000100280.17 ENST00000432560.6 9.155674 1 2.479480e-03
15282 ENSG00000145335.17 ENST00000394991.8 9.152158 1 2.484249e-03
6683 ENSG00000145390.12 ENST00000692078.1 9.146993 1 2.491271e-03
19301 ENSG00000168275.16 ENST00000366613.1 9.146987 1 2.491279e-03
19302 ENSG00000168275.16 ENST00000619305.1 9.146987 1 2.491279e-03
19765 ENSG00000132424.17 ENST00000460600.1 9.144387 1 2.494822e-03
14981 ENSG00000176473.14 ENST00000335290.10 9.142848 1 2.496922e-03
15342 ENSG00000083312.19 ENST00000506351.6 9.114580 1 2.535802e-03
21959 ENSG00000146267.12 ENST00000480148.1 9.110185 1 2.541901e-03
3416 ENSG00000132604.11 ENST00000254942.8 9.100685 1 2.555138e-03
3417 ENSG00000132604.11 ENST00000569584.6 9.100685 1 2.555138e-03
20435 ENSG00000163873.10 ENST00000373091.8 9.065536 1 2.604722e-03
20436 ENSG00000163873.10 ENST00000373093.4 9.065536 1 2.604722e-03
5442 ENSG00000071127.17 ENST00000499869.7 9.054087 1 2.621082e-03
5441 ENSG00000071127.17 ENST00000382452.6 9.054087 1 2.621082e-03
16528 ENSG00000181450.18 ENST00000343776.10 9.046754 1 2.631617e-03
16529 ENSG00000181450.18 ENST00000397097.4 9.046754 1 2.631617e-03
8150 ENSG00000160191.18 ENST00000291539.11 9.042878 1 2.637202e-03
8151 ENSG00000160191.18 ENST00000335512.8 9.042878 1 2.637202e-03
15447 ENSG00000142599.19 ENST00000377464.5 9.036829 1 2.645942e-03
23323 ENSG00000162923.17 ENST00000678555.1 9.035807 1 2.647422e-03
23322 ENSG00000162923.17 ENST00000651911.2 9.035807 1 2.647422e-03
4443 ENSG00000037280.16 ENST00000393347.7 9.033175 1 2.651235e-03
4442 ENSG00000037280.16 ENST00000261937.11 9.033175 1 2.651235e-03
3709 ENSG00000115317.12 ENST00000258080.8 9.030999 1 2.654393e-03
25409 ENSG00000146067.16 ENST00000510479.5 9.024947 1 2.663196e-03
8195 ENSG00000105227.16 ENST00000324001.8 9.020590 1 2.669553e-03
15599 ENSG00000116288.13 ENST00000338639.10 9.015945 1 2.676344e-03
12753 ENSG00000106462.12 ENST00000350995.6 9.006579 1 2.690095e-03
8745 ENSG00000163697.17 ENST00000513611.5 9.006519 1 2.690184e-03
15156 ENSG00000131748.16 ENST00000394250.8 9.001631 1 2.697388e-03
17248 ENSG00000128585.18 ENST00000352689.11 9.000485 1 2.699079e-03
6978 ENSG00000148948.8 ENST00000528697.6 8.982051 1 2.726445e-03
17740 ENSG00000187239.17 ENST00000446176.7 8.978089 1 2.732363e-03
10028 ENSG00000170638.10 ENST00000303434.8 8.976870 1 2.734186e-03
5 ENSG00000256591.5 ENST00000536670.5 8.976249 1 2.735116e-03
13448 ENSG00000221988.13 ENST00000324816.11 8.973841 1 2.738723e-03
9609 ENSG00000109103.12 ENST00000470125.5 8.972812 1 2.740266e-03
1959 ENSG00000114857.19 ENST00000232978.13 8.967843 1 2.747728e-03
1960 ENSG00000114857.19 ENST00000429888.5 8.967843 1 2.747728e-03
25516 ENSG00000249859.13 ENST00000653522.1 8.961440 1 2.757375e-03
11669 ENSG00000168395.16 ENST00000313552.11 8.960526 1 2.758755e-03
11670 ENSG00000168395.16 ENST00000636051.1 8.960526 1 2.758755e-03
663 ENSG00000079156.17 ENST00000409045.7 8.948353 1 2.777198e-03
7235 ENSG00000151491.14 ENST00000647224.1 8.945626 1 2.781347e-03
16950 ENSG00000003756.17 ENST00000347869.8 8.926481 1 2.810653e-03
11063 ENSG00000003402.21 ENST00000423241.6 8.924514 1 2.813682e-03
14157 ENSG00000184809.13 ENST00000380604.8 8.919257 1 2.821792e-03
11901 ENSG00000110497.15 ENST00000534300.5 8.918886 1 2.822366e-03
5168 ENSG00000077232.19 ENST00000616986.5 8.917455 1 2.824578e-03
22972 ENSG00000204406.14 ENST00000638043.2 8.903895 1 2.845630e-03
15618 ENSG00000182568.17 ENST00000454909.6 8.900516 1 2.850901e-03
24701 ENSG00000183666.18 ENST00000691699.1 8.882002 1 2.879956e-03
21796 ENSG00000134490.14 ENST00000383233.8 8.878187 1 2.885980e-03
13011 ENSG00000177700.6 ENST00000322028.5 8.875163 1 2.890764e-03
13012 ENSG00000177700.6 ENST00000534030.1 8.875163 1 2.890764e-03
17674 ENSG00000198055.11 ENST00000355958.9 8.872626 1 2.894784e-03
12550 ENSG00000137343.18 ENST00000318999.11 8.870962 1 2.897424e-03
13472 ENSG00000158560.14 ENST00000359388.8 8.865729 1 2.905741e-03
18150 ENSG00000005810.19 ENST00000357337.11 8.859711 1 2.915338e-03
21399 ENSG00000124786.12 ENST00000648987.1 8.852532 1 2.926826e-03
3250 ENSG00000131016.17 ENST00000359755.5 8.849706 1 2.931361e-03
4135 ENSG00000091039.17 ENST00000393249.6 8.838406 1 2.949567e-03
18344 ENSG00000197694.18 ENST00000372739.7 8.835573 1 2.954149e-03
2654 ENSG00000125744.12 ENST00000430715.6 8.835039 1 2.955012e-03
22609 ENSG00000253846.3 ENST00000612503.1 8.832182 1 2.959644e-03
22608 ENSG00000253846.3 ENST00000398610.3 8.832182 1 2.959644e-03
5050 ENSG00000129810.15 ENST00000263753.8 8.823958 1 2.973012e-03
17132 ENSG00000143612.21 ENST00000368521.10 8.800514 1 3.011457e-03
23216 ENSG00000224032.8 ENST00000688370.1 8.797361 1 3.016666e-03
4468 ENSG00000050426.16 ENST00000623495.1 8.795010 1 3.020556e-03
16706 ENSG00000188732.11 ENST00000409653.5 8.791454 1 3.026450e-03
14778 ENSG00000094631.21 ENST00000334136.11 8.789190 1 3.030208e-03
14779 ENSG00000094631.21 ENST00000644068.1 8.789190 1 3.030208e-03
6151 ENSG00000140990.15 ENST00000268668.11 8.785849 1 3.035762e-03
3262 ENSG00000131089.17 ENST00000671741.2 8.784343 1 3.038269e-03
952 ENSG00000100425.19 ENST00000404034.5 8.780074 1 3.045389e-03
953 ENSG00000100425.19 ENST00000404760.6 8.780074 1 3.045389e-03
16803 ENSG00000120899.18 ENST00000346049.10 8.774755 1 3.054283e-03
16804 ENSG00000120899.18 ENST00000397501.5 8.774755 1 3.054283e-03
21492 ENSG00000168994.14 ENST00000380277.6 8.774396 1 3.054883e-03
21493 ENSG00000168994.14 ENST00000380283.5 8.774396 1 3.054883e-03
11917 ENSG00000164306.11 ENST00000314970.11 8.773145 1 3.056978e-03
18663 ENSG00000140511.12 ENST00000359595.8 8.768662 1 3.064501e-03
18664 ENSG00000140511.12 ENST00000558770.5 8.768662 1 3.064501e-03
23562 ENSG00000213988.11 ENST00000418063.3 8.766507 1 3.068124e-03
3566 ENSG00000134245.18 ENST00000369686.9 8.748763 1 3.098121e-03
25615 ENSG00000196951.12 ENST00000664103.1 8.742640 1 3.108541e-03
15819 ENSG00000166348.20 ENST00000418501.5 8.732948 1 3.125109e-03
24906 ENSG00000135253.16 ENST00000610776.5 8.732079 1 3.126598e-03
18008 ENSG00000196531.14 ENST00000678376.1 8.731530 1 3.127539e-03
17474 ENSG00000129007.16 ENST00000395463.3 8.730318 1 3.129620e-03
3897 ENSG00000136717.15 ENST00000409400.1 8.727832 1 3.133888e-03
10233 ENSG00000168672.4 ENST00000304916.4 8.715625 1 3.154943e-03
10234 ENSG00000168672.4 ENST00000652209.1 8.715625 1 3.154943e-03
9684 ENSG00000167703.15 ENST00000412517.3 8.708225 1 3.167774e-03
18733 ENSG00000196562.15 ENST00000495544.5 8.702738 1 3.177324e-03
18734 ENSG00000196562.15 ENST00000688720.1 8.702738 1 3.177324e-03
22860 ENSG00000138081.22 ENST00000493962.6 8.700002 1 3.182096e-03
9202 ENSG00000165689.17 ENST00000298537.11 8.699410 1 3.183131e-03
5935 ENSG00000072041.18 ENST00000266682.10 8.699050 1 3.183759e-03
7892 ENSG00000157764.14 ENST00000496384.7 8.690207 1 3.199243e-03
7893 ENSG00000157764.14 ENST00000642228.1 8.690207 1 3.199243e-03
353 ENSG00000010818.10 ENST00000367603.8 8.680831 1 3.215743e-03
354 ENSG00000010818.10 ENST00000367604.6 8.680831 1 3.215743e-03
18185 ENSG00000196843.17 ENST00000357485.8 8.672433 1 3.230595e-03
18186 ENSG00000196843.17 ENST00000412735.5 8.672433 1 3.230595e-03
20855 ENSG00000095739.11 ENST00000375533.6 8.670763 1 3.233557e-03
20856 ENSG00000095739.11 ENST00000497699.1 8.670763 1 3.233557e-03
13605 ENSG00000128699.14 ENST00000325795.7 8.667751 1 3.238907e-03
11190 ENSG00000172992.13 ENST00000452796.7 8.660622 1 3.251602e-03
13933 ENSG00000174010.10 ENST00000689334.1 8.651477 1 3.267964e-03
17662 ENSG00000198270.13 ENST00000437003.3 8.641127 1 3.286581e-03
3098 ENSG00000100056.12 ENST00000252137.11 8.639051 1 3.290328e-03
17055 ENSG00000126012.13 ENST00000404049.7 8.636311 1 3.295280e-03
9941 ENSG00000108312.15 ENST00000529383.5 8.635474 1 3.296794e-03
16974 ENSG00000119139.21 ENST00000650084.1 8.631088 1 3.304742e-03
9700 ENSG00000161551.15 ENST00000640955.1 8.629034 1 3.308469e-03
6451 ENSG00000143569.19 ENST00000343815.10 8.627448 1 3.311351e-03
2222 ENSG00000119640.9 ENST00000555135.1 8.625221 1 3.315402e-03
1099 ENSG00000102081.16 ENST00000370477.5 8.609725 1 3.343728e-03
5714 ENSG00000104691.16 ENST00000380154.9 8.591840 1 3.376726e-03
5713 ENSG00000104691.16 ENST00000265616.10 8.591840 1 3.376726e-03
17572 ENSG00000179454.14 ENST00000355081.3 8.585779 1 3.387984e-03
17573 ENSG00000179454.14 ENST00000396128.9 8.585779 1 3.387984e-03
4894 ENSG00000099889.14 ENST00000406522.5 8.570767 1 3.416032e-03
21317 ENSG00000105672.15 ENST00000403402.1 8.562115 1 3.432304e-03
23335 ENSG00000144426.19 ENST00000683650.1 8.561092 1 3.434234e-03
20225 ENSG00000173269.14 ENST00000372027.10 8.545749 1 3.463300e-03
20226 ENSG00000173269.14 ENST00000474994.2 8.545749 1 3.463300e-03
15574 ENSG00000153130.18 ENST00000506597.2 8.545295 1 3.464165e-03
3574 ENSG00000134285.11 ENST00000551694.5 8.544329 1 3.466004e-03
3178 ENSG00000169955.8 ENST00000252799.3 8.542212 1 3.470036e-03
17177 ENSG00000169062.15 ENST00000351487.5 8.538363 1 3.477383e-03
14141 ENSG00000072736.19 ENST00000349223.9 8.536130 1 3.481651e-03
23508 ENSG00000244625.7 ENST00000435162.5 8.529770 1 3.493839e-03
18318 ENSG00000196730.13 ENST00000408954.8 8.513541 1 3.525134e-03
18319 ENSG00000196730.13 ENST00000472284.5 8.513541 1 3.525134e-03
23563 ENSG00000213988.11 ENST00000469078.5 8.510144 1 3.531720e-03
5192 ENSG00000058085.15 ENST00000264144.5 8.508282 1 3.535336e-03
5193 ENSG00000058085.15 ENST00000493293.5 8.508282 1 3.535336e-03
2394 ENSG00000122218.16 ENST00000650154.1 8.493664 1 3.563855e-03
23164 ENSG00000232677.10 ENST00000591372.3 8.493191 1 3.564781e-03
11521 ENSG00000112763.17 ENST00000429381.5 8.489348 1 3.572319e-03
19815 ENSG00000064703.13 ENST00000369702.5 8.488964 1 3.573072e-03
19156 ENSG00000169851.15 ENST00000543491.2 8.477065 1 3.596518e-03
24931 ENSG00000175697.11 ENST00000464295.6 8.471998 1 3.606551e-03
9246 ENSG00000011114.15 ENST00000298896.7 8.471617 1 3.607305e-03
6598 ENSG00000144840.10 ENST00000473654.5 8.463709 1 3.623024e-03
adj_pvalue
20181 8.966705e-61
20182 8.966705e-61
13318 3.386678e-37
10876 1.300533e-32
10877 1.300533e-32
11418 1.411698e-31
15051 3.845568e-26
15050 3.845568e-26
14800 5.945456e-26
20211 2.918915e-25
10201 1.874511e-24
10200 1.874511e-24
3630 2.020712e-23
3631 2.020712e-23
15240 4.477342e-23
4948 1.058164e-21
13317 1.368779e-20
20718 8.134032e-20
7543 1.469346e-19
21528 2.497172e-19
15239 1.043322e-18
20078 5.110969e-18
20077 5.110969e-18
20748 6.174915e-17
181 6.924383e-17
15063 9.526181e-17
15064 9.526181e-17
16811 8.763323e-16
4483 1.573807e-15
5180 2.884724e-15
13015 4.882499e-15
19376 4.882499e-15
13013 8.442157e-15
2420 2.797715e-14
2421 2.797715e-14
15672 1.377536e-13
15671 1.377536e-13
16563 2.654583e-13
8818 3.147295e-13
8819 3.147295e-13
7209 3.847790e-13
7208 3.847790e-13
4946 8.479721e-13
7852 1.144944e-11
7853 1.144944e-11
14822 1.422366e-11
15398 2.387561e-11
5048 2.948141e-11
9648 3.237754e-11
6702 3.318498e-11
23244 3.767872e-11
18915 5.483756e-11
18916 5.483756e-11
19378 1.178429e-10
15879 1.213319e-10
8391 2.507672e-10
12615 3.923652e-10
18619 4.004879e-10
6481 1.305394e-09
6480 1.305394e-09
3534 1.703501e-09
20745 1.718749e-09
5178 1.849278e-09
1118 2.352399e-09
15006 2.651967e-09
15007 2.651967e-09
21530 3.098336e-09
7088 3.491698e-09
7087 3.491698e-09
12301 3.499402e-09
1744 3.753644e-09
1745 3.753644e-09
17087 4.492818e-09
722 4.492818e-09
723 4.492818e-09
16181 5.072620e-09
16182 5.072620e-09
16562 5.788938e-09
4354 6.382609e-09
10498 6.382609e-09
10499 6.382609e-09
18805 6.574973e-09
18806 6.574973e-09
10623 6.754448e-09
10624 6.754448e-09
14091 8.963657e-09
14824 9.638510e-09
16862 1.025531e-08
1112 1.049317e-08
1111 1.049317e-08
22233 1.061817e-08
1480 1.201556e-08
1479 1.201556e-08
401 1.205514e-08
17131 1.677511e-08
13275 2.103824e-08
23401 2.489636e-08
21618 2.516249e-08
8743 2.715607e-08
16810 2.846341e-08
16015 2.846341e-08
6782 3.232253e-08
10415 3.666058e-08
5623 4.259372e-08
18038 4.350677e-08
18039 4.350677e-08
7745 4.494490e-08
7746 4.494490e-08
12051 5.242655e-08
16702 5.242655e-08
16703 5.242655e-08
8723 5.644398e-08
2037 5.744250e-08
7544 5.939982e-08
180 6.175234e-08
2899 6.491486e-08
2898 6.491486e-08
3293 7.904912e-08
22386 7.923710e-08
962 9.156028e-08
24977 1.170033e-07
15881 1.187444e-07
8394 1.254443e-07
18168 1.286850e-07
11592 1.439437e-07
6733 1.558159e-07
12170 1.558159e-07
12171 1.558159e-07
182 1.659139e-07
18398 1.710459e-07
22234 1.712289e-07
16858 1.712289e-07
16859 1.712289e-07
20209 2.671879e-07
20210 2.671879e-07
23243 3.622038e-07
17197 4.408653e-07
14329 4.467719e-07
14328 4.467719e-07
1718 4.467719e-07
1719 4.467719e-07
15716 5.026104e-07
19155 5.637010e-07
4252 5.771253e-07
4253 5.771253e-07
12052 5.771253e-07
17089 6.608598e-07
3923 6.837179e-07
22965 7.113876e-07
22966 7.113876e-07
15279 7.603156e-07
15280 7.603156e-07
17824 8.459178e-07
15276 8.621333e-07
15399 8.860081e-07
3533 9.146050e-07
13947 9.271961e-07
18873 9.691060e-07
22152 9.798490e-07
11479 1.123892e-06
11478 1.123892e-06
18617 1.231979e-06
15067 1.302313e-06
6854 1.330895e-06
6853 1.330895e-06
12577 1.424189e-06
16669 1.424189e-06
16670 1.424189e-06
19476 1.497034e-06
19477 1.497034e-06
8009 1.554455e-06
6734 1.793965e-06
166 1.841974e-06
14124 1.894787e-06
14361 1.898286e-06
11295 1.898286e-06
11296 1.898286e-06
6799 1.914937e-06
16852 1.914937e-06
16853 1.914937e-06
4087 1.995825e-06
12613 2.071319e-06
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10028 4.058579e-02
5 4.058579e-02
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1959 4.065212e-02
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25516 4.072476e-02
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11670 4.072476e-02
663 4.096675e-02
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12550 4.230281e-02
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3250 4.267353e-02
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5714 4.706445e-02
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17572 4.715555e-02
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4894 4.751282e-02
21317 4.769955e-02
23335 4.769955e-02
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18318 4.862397e-02
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23563 4.866387e-02
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2394 4.900163e-02
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11521 4.904808e-02
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24931 4.941613e-02
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6598 4.959743e-02
[1] 1459
pvalue may contain NA values which may cause downstream errors (in stagewise analysis by stageR) so they are converted to 1`s.
Plotting
For a given gene, plot the observed and estimated with Dirichlet-multinomial model feature proportions in each group. Estimated group proportions are marked with diamond shapes.
Warning: The `<scale>` argument of `guides()` cannot be `FALSE`. Use "none" instead as
of ggplot2 3.3.4.
ℹ The deprecated feature was likely used in the DRIMSeq package.
Please report the issue to the authors.
Coordinate system already present. Adding new coordinate system, which will
replace the existing one.
StageR following DRIMSeq
stageR package does stage-wise analysis of data, by screening first at the gene level for evidence of DTU (screening stage) and confirms which trancsripts within those significant genes show evidence of DTU (confirmation stage).
A vector of per-gene p-values pScreen for the screening stage is constructed. Addiionally, the gene and transcript version numbers are stripped from their Ensembl IDs (only first 15 characters are kept).
A one column matrix of the confirmation p-values pConfirmation is constructed:
A two column dataframe tx2genewith the transcript and gene identifiers is arranged:
stageR analysis is perform with overall false discovery rate (OFDR, alpha parameter) equal to 0.05.
stageRObj <- stageRTx(pScreen=pScreen, pConfirmation=pConfirmation,
pScreenAdjusted=FALSE, tx2gene=tx2gene)
stageRObj <- stageWiseAdjustment(stageRObj, method="dtu", alpha=0.05)
suppressWarnings({
drim.padj <- getAdjustedPValues(stageRObj, order=FALSE,
onlySignificantGenes=TRUE)
})The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.
geneID txID gene transcript
1 ENSG00000112759 ENST00000371755 8.889936e-61 0.000000e+00
2 ENSG00000112759 ENST00000393844 8.889936e-61 0.000000e+00
3 ENSG00000107554 ENST00000543621 1.221282e-36 5.097696e-40
4 ENSG00000172889 ENST00000371698 6.446990e-33 0.000000e+00
5 ENSG00000172889 ENST00000406555 6.446990e-33 0.000000e+00
6 ENSG00000164587 ENST00000312037 1.866405e-31 4.249832e-34
[1] 3149
The data.frame dex.padj summarizes the adjusted p-values from the two-stage analysis. Only genes that passed the filter (screening) are included in the table. The transcripts (column trancsript) with values less than 0.05 (5 % OFDR) pass the confirmation stage.
DEXSeq
The filtered DRIMSeq object is used for DEXSeq workflow, as the filtering is easier, and the analysis is sped up. DEXSeqDataSet is built from d, filtered DRIMseq object, sample information (sample.data), a design formula, transcript ID and gene ID:
sample.data <- DRIMSeq::samples(d)
# We start with already filtered DRIMSeq object
count.data <- round(as.matrix(counts(d)[,-c(1:2)]))
dxd <- DEXSeqDataSet(countData=count.data,
sampleData=sample.data,
design=~sample + exon + day:exon,
featureID=counts(d)$feature_id,
groupID=counts(d)$gene_id)converting counts to integer mode
Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors
DEXSeq analysis is performed using the following 3 functions: (1) estimation of size factors using estimateSizeFactors, (2) estimation of dispersion estimateDispersions, then (3) perform a likelihood ratio test for differential exon usage (in this case, transcripts) testForDEU.
system.time({
dxd <- estimateSizeFactors(dxd)
dxd <- estimateDispersions(dxd, quiet=TRUE)
dxd <- testForDEU(dxd, reducedModel=~sample + exon)
})24 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT
user system elapsed
129.169 0.180 129.493
The results tables (log2 fold changes and p-values) can be generated using the DEXSeqResultsfunction and perGeneQValue function is used to compute a per-gene adjusted p-value.
dxr <- DEXSeqResults(dxd, independentFiltering=FALSE)
qval <- perGeneQValue(dxr)
# Per gene
dxr.g <- data.frame(gene=names(qval),qval)
# Per transcript
dxr.t = as.data.frame(dxr[, c("featureID","groupID","pvalue")])
head(dxr.g) gene qval
ENSG00000000005.6 ENSG00000000005.6 1.000000e+00
ENSG00000000457.14 ENSG00000000457.14 9.537975e-01
ENSG00000000460.17 ENSG00000000460.17 9.362627e-08
ENSG00000001084.13 ENSG00000001084.13 3.136415e-01
ENSG00000001167.15 ENSG00000001167.15 1.000000e+00
ENSG00000001460.18 ENSG00000001460.18 1.198466e-01
Results:
[1] 1457
[1] 2409
stageR following DEXSeq
The code for the procedure is similar to DRIMSeq procedure, with alpha=0.05.
strp <- function(x) substr(x,1,15)
pConfirmation <- matrix(dxr$pvalue,ncol=1)
dimnames(pConfirmation) <- list(strp(dxr$featureID),"transcript")
pScreen <- qval
names(pScreen) <- strp(names(pScreen))
tx2gene <- data.frame(dxr.t[,c("featureID", "groupID")],
dxr.t[,c("featureID", "groupID")])
for (i in 1:2) tx2gene[,i] = strp(tx2gene[,i])
stageRObj <- stageRTx(pScreen=pScreen, pConfirmation=pConfirmation,
pScreenAdjusted=TRUE, tx2gene=tx2gene[1:2])
stageRObj = stageRTx(pScreen = pScreen,
pConfirmation = pConfirmation,
pScreenAdjusted = TRUE,
tx2gene = tx2gene[1:2])
stageRObj = stageWiseAdjustment(stageRObj, method = "dtu", alpha = 0.05)
suppressWarnings({
dex.padj <- getAdjustedPValues(stageRObj, order=FALSE,
onlySignificantGenes=TRUE)
})The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.
dex.padj = merge(tx2gene, dex.padj, by.x = c("groupID","featureID"), by.y = c("geneID","txID"))
head(dex.padj) groupID featureID featureID.1 groupID.1
1 ENSG00000000460 BambuTx12 BambuTx12 ENSG00000000460.17
2 ENSG00000000460 ENST00000359326 ENST00000359326.9 ENSG00000000460.17
3 ENSG00000001497 ENST00000374807 ENST00000374807.9 ENSG00000001497.18
4 ENSG00000001497 ENST00000374811 ENST00000374811.8 ENSG00000001497.18
5 ENSG00000001497 ENST00000677834 ENST00000677834.1 ENSG00000001497.18
6 ENSG00000001497 ENST00000678602 ENST00000678602.1 ENSG00000001497.18
gene transcript
1 9.362627e-08 0.000000e+00
2 9.362627e-08 0.000000e+00
3 2.793368e-11 2.037362e-04
4 2.793368e-11 2.467069e-12
5 2.793368e-11 2.037362e-04
6 2.793368e-11 1.000000e+00
Exporting the results
dex.norm = cbind(as.data.frame(stringr::str_split_fixed(rownames(counts(dxd)), ":", 2)), as.data.frame(counts(dxd, normalized = TRUE))[,1:20])
colnames(dex.norm) = c("groupID", "featureID", as.character(colData(dxd)$sample_id)[1:20])
row.names(dex.norm) = NULL
# Per-group normalised mean
dex.mean = as.data.frame(sapply( levels(samps$day),
function(lvl) rowMeans(dex.norm[, 3:ncol(dex.norm)][, samps$day == lvl, drop = FALSE]) ))
colnames(dex.mean) <- paste0("mean.day", colnames(dex.mean))
# log2 fold change in expression
dex.log2fc = log2(dex.mean[2]/dex.mean[1])
colnames(dex.log2fc) = "log2fc"
rownames(dex.log2fc) = dex.norm$featureID
# Merge to create result data
dexData = cbind(dex.norm[,1:2], dex.mean, dex.norm[, 3:ncol(dex.norm)])
colnames(dexData)[1:2] <- c("GeneID","TranscriptID")
dexData = dexData[order(dexData$GeneID, dexData$TranscriptID),]
# Merge to create result data
dexDTU = merge(dex.padj[,c("featureID.1","groupID.1","gene","transcript")], dex.log2fc, by.x = "featureID.1", by.y = "row.names")
colnames(dexDTU)[1:2] <- c("TranscriptID","GeneID")
dexDTU = dexDTU[order(dexDTU$GeneID, dexDTU$TranscriptID),]
# Write results to files
write.table(dexData, file="DTU_DEXSeq-stageR_means_and_counts.txt", sep = "\t", quote = F, row.names = F, col.names = T)
write.table(dexDTU, file="DTU_DEXSeq-stageR_results.txt", sep = "\t", quote = F, row.names = F, col.names = T)Plotting
A custom function plotExpression was made to plot the transcript expression of a given gene as from .
# We will use this function in both DRIMSeq & DEXSeq workflows
plotExpression <- function(expData = NULL, geneID = NULL, samps = NULL, isProportion = FALSE) {
colnames(expData)[1:2] = c("gid","tid")
sub = subset(expData, gid == geneID)
print(sub)
sub = reshape2::melt(sub, id = c("gid", "tid"))
sub = merge(samps, sub, by.x = "sample_id", by.y = "variable")
print(sub)
if(!isProportion) {
sub$value = log(sub$value)
}
print(sub)
clrs = c("dodgerblue3", "maroon2", "forestgreen", "darkorange1", "blueviolet", "firebrick2",
"deepskyblue", "orchid2", "chartreuse3", "gold", "slateblue1", "tomato" , "blue", "magenta", "green3",
"yellow", "purple3", "red" ,"darkslategray1", "lightpink1", "lightgreen", "khaki1", "plum3", "salmon")
p = ggplot(sub, aes(tid, value, color = day, fill = day)) +
geom_boxplot(alpha = 0.4, outlier.shape = NA, width = 0.8, lwd = 0.5) +
stat_summary(fun = mean, geom = "point", color = "black", shape = 5, size = 3, position=position_dodge(width = 0.8)) +
scale_color_manual(values = clrs) + scale_fill_manual(values = clrs) +
geom_quasirandom(color = "black", size = 1, dodge.width = 0.8) + theme_bw() +
ggtitle(geneID) + xlab("Transcripts")
if(!isProportion) {
p = p + ylab("log(Expression)")
} else {
p = p + ylab("Proportions")
}
p
}# Plot the normalised counts for one of the significant genes, where we can see evidence of switching
gene_id <- unique(dex.padj[order(dex.padj$transcript, dex.padj$gene),]$groupID.1)[1]
plotExpression(dex.norm, gene_id, samps, isProportion = T) gid tid day0.rep1 day0.rep2 day0.rep3
10848 ENSG00000010671.17 ENST00000308731.8 0.00000 0.00000 0.00000
10849 ENSG00000010671.17 ENST00000621635.4 34.31592 18.37981 21.88111
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
10848 3.851982 62.56142 915.4916 849.848827 2210.95863 2283.79343 1188.60736
10849 33.704846 0.00000 0.0000 8.484348 57.94087 28.49262 46.59708
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
10848 1114.01421 34.31592 18.37981 21.88111 33.704846 0.00000
10849 41.62983 0.00000 0.00000 0.00000 3.851982 62.56142
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
10848 0.0000 8.484348 57.94087 28.49262
10849 915.4916 849.848827 2210.95863 2283.79343
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.315922
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.379814
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.881106
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.851982
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.704846
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.561421
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.491563
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.848827
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.484348
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.940870
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.492624
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.597075
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.629829
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.315922
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.379814
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.881106
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.851982
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.704846
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.561421
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.491563
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.848827
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.484348
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.940870
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.492624
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.597075
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.629829
Comparison of DRIMSeq and DEXSeq
Number of identified transcripts from DEXSeq:
Number of identified transcripts from DRIMSeq:
Check the intersection between the different methods for screened genes:
[1] 553
Check the intersection between the different methods for features:
Making a function for the pipeline using DEXSeq x DRIMSeq
samps <- df_list_meta$metadata
samps <- samps %>% column_to_rownames(var="sampleID")
colnames(samps) <- c("sample_id", "day")
samps$day <- factor(samps$day)
DTU <- function(salmon, txdf, sample_name, n = 11, n.small = 11){
# DRIMSeq Filtering
cts <- salmon
colnames(cts) <- samps$sample_id
counts <- data.frame(gene_id=txdf$gene_id,
feature_id=rownames(txdf),
cts)
d <- dmDSdata(counts=counts, samples=samps)
d <- dmFilter(d,
min_samps_feature_expr=n.small, min_feature_expr=10,
min_samps_feature_prop=n.small, min_feature_prop=0.1,
min_samps_gene_expr=n, min_gene_expr=10)
print(plotData(d))
png(paste0(sample_name, "plotData.DEXSeq-stageR.png"), width=6, height=6, units = "in", res = 300)
print(plotData(d))
dev.off()
print(table(table(counts(d)$gene_id)))
sample.data <- DRIMSeq::samples(d)
# DEXSeq
count.data <- round(as.matrix(counts(d)[,-c(1:2)]))
dxd <- DEXSeqDataSet(countData=count.data,
sampleData=sample.data,
design=~sample + exon + day:exon,
featureID=counts(d)$feature_id,
groupID=counts(d)$gene_id)
dxd <- estimateSizeFactors(dxd)
dxd <- estimateDispersions(dxd, quiet=TRUE)
dxd <- testForDEU(dxd, reducedModel=~sample + exon)
dxr <- DEXSeqResults(dxd, independentFiltering=FALSE)
qval <- perGeneQValue(dxr)
# Per gene
dxr.g <- data.frame(gene=names(qval),qval)
# Per transcript
dxr.t = as.data.frame(dxr[, c("featureID","groupID","pvalue")])
# Number of identified genes showing evidence for DTU
print(nrow(dxr.g[dxr.g$qval < 0.05,]))
# Number of transcripts involved
print(nrow(dxr[dxr$padj < 0.05,]))
# stageR
strp <- function(x) substr(x,1,15)
pConfirmation <- matrix(dxr$pvalue,ncol=1)
dimnames(pConfirmation) <- list(strp(dxr$featureID),"transcript")
pScreen <- qval
names(pScreen) <- strp(names(pScreen))
tx2gene <- data.frame(dxr.t[,c("featureID", "groupID")],
dxr.t[,c("featureID", "groupID")])
for (i in 1:2) tx2gene[,i] = strp(tx2gene[,i])
stageRObj <- stageRTx(pScreen=pScreen, pConfirmation=pConfirmation,
pScreenAdjusted=TRUE, tx2gene=tx2gene[1:2])
stageRObj = stageRTx(pScreen = pScreen,
pConfirmation = pConfirmation,
pScreenAdjusted = TRUE,
tx2gene = tx2gene[1:2])
stageRObj = stageWiseAdjustment(stageRObj, method = "dtu", alpha = 0.05)
suppressWarnings({
dex.padj <- getAdjustedPValues(stageRObj, order=FALSE,
onlySignificantGenes=TRUE)
})
dex.padj = merge(tx2gene, dex.padj, by.x = c("groupID","featureID"), by.y = c("geneID","txID"))
print(head(dex.padj[order(dex.padj$gene, decreasing = T), ]))
# Normalize counts
dex.norm = cbind(as.data.frame(stringr::str_split_fixed(rownames(counts(dxd)), ":", 2)), as.data.frame(counts(dxd, normalized = TRUE))[,1:20])
colnames(dex.norm) = c("groupID", "featureID", as.character(colData(dxd)$sample_id)[1:20])
row.names(dex.norm) = NULL
# Per-group normalised mean
dex.mean = as.data.frame(sapply( levels(samps$day),
function(lvl) rowMeans(dex.norm[, 3:ncol(dex.norm)][, samps$day == lvl, drop = FALSE]) ))
colnames(dex.mean) <- paste0("mean.day", colnames(dex.mean))
# log2 fold change in expression
dex.log2fc = log2(dex.mean[2]/dex.mean[1])
colnames(dex.log2fc) = "log2fc"
rownames(dex.log2fc) = dex.norm$featureID
# Merge to create result data
dexData = cbind(dex.norm[,1:2], dex.mean, dex.norm[, 3:ncol(dex.norm)])
colnames(dexData)[1:2] <- c("GeneID","TranscriptID")
dexData = dexData[order(dexData$GeneID, dexData$TranscriptID),]
# Merge to create result data
dexDTU = merge(dex.padj[,c("featureID.1","groupID.1","gene","transcript")], dex.log2fc, by.x = "featureID.1", by.y = "row.names")
colnames(dexDTU)[1:2] <- c("TranscriptID","GeneID")
dexDTU = dexDTU[order(dexDTU$GeneID, dexDTU$TranscriptID),]
# Write results to files
write.table(dexData, file=paste0(sample_name, "DTU_DEXSeq-stageR_means_and_counts.txt"), sep = "\t", quote = F, row.names = F, col.names = T)
write.table(dexDTU, file=paste0(sample_name, "DTU_DEXSeq-stageR_results.txt"), sep = "\t", quote = F, row.names = F, col.names = T)
# Plot the normalised counts for one of the significant genes, where we can see evidence of switching
gene_id <- unique(dex.padj[order(dex.padj$transcript, dex.padj$gene),]$groupID.1)[1]
print(plotExpression(dex.norm, gene_id, samps, isProportion = T))
png(paste0(sample_name, "plotExpression-stageR.png"), width=6, height=6, units = "in", res = 300)
print(plotExpression(dex.norm, gene_id, samps, isProportion = T))
dev.off()
return(dexDTU)
}NDR 0.025
# Transcript to gene mappings
txdf <- df_list_meta$metagenes_0.025
res_salmon_0.025 <- DTU(salmon_0.025, txdf, "salmon_0.025.", n = 3, n.small = 3)
2 3 4 5 6 7 8 9
5214 2887 1213 433 114 29 8 3
converting counts to integer mode
Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors
24 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT
[1] 1457
[1] 2409
The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.
groupID featureID featureID.1 groupID.1
3614 ENSG00000179603 ENST00000339582 ENST00000339582.7 ENSG00000179603.18
3615 ENSG00000179603 ENST00000358373 ENST00000358373.7 ENSG00000179603.18
3616 ENSG00000179603 ENST00000457830 ENST00000457830.1 ENSG00000179603.18
3617 ENSG00000179603 ENST00000472701 ENST00000472701.5 ENSG00000179603.18
2982 ENSG00000164162 ENST00000309439 ENST00000309439.9 ENSG00000164162.14
2983 ENSG00000164162 ENST00000451299 ENST00000451299.6 ENSG00000164162.14
gene transcript
3614 0.04999221 0.63208638
3615 0.04999221 0.03665347
3616 0.04999221 1.00000000
3617 0.04999221 0.04462491
2982 0.04992877 1.00000000
2983 0.04992877 0.03658163
gid tid day0.rep1 day0.rep2 day0.rep3
10848 ENSG00000010671.17 ENST00000308731.8 0.00000 0.00000 0.00000
10849 ENSG00000010671.17 ENST00000621635.4 34.31592 18.37981 21.88111
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
10848 3.851982 62.56142 915.4916 849.848827 2210.95863 2283.79343 1188.60736
10849 33.704846 0.00000 0.0000 8.484348 57.94087 28.49262 46.59708
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
10848 1114.01421 34.31592 18.37981 21.88111 33.704846 0.00000
10849 41.62983 0.00000 0.00000 0.00000 3.851982 62.56142
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
10848 0.0000 8.484348 57.94087 28.49262
10849 915.4916 849.848827 2210.95863 2283.79343
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.315922
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.379814
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.881106
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.851982
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.704846
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.561421
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.491563
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.848827
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.484348
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.940870
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.492624
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.597075
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.629829
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.315922
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.379814
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.881106
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.851982
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.704846
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.561421
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.491563
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.848827
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.484348
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.940870
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.492624
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.597075
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.629829
gid tid day0.rep1 day0.rep2 day0.rep3
10848 ENSG00000010671.17 ENST00000308731.8 0.00000 0.00000 0.00000
10849 ENSG00000010671.17 ENST00000621635.4 34.31592 18.37981 21.88111
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
10848 3.851982 62.56142 915.4916 849.848827 2210.95863 2283.79343 1188.60736
10849 33.704846 0.00000 0.0000 8.484348 57.94087 28.49262 46.59708
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
10848 1114.01421 34.31592 18.37981 21.88111 33.704846 0.00000
10849 41.62983 0.00000 0.00000 0.00000 3.851982 62.56142
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
10848 0.0000 8.484348 57.94087 28.49262
10849 915.4916 849.848827 2210.95863 2283.79343
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.315922
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.379814
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.881106
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.851982
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.704846
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.561421
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.491563
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.848827
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.484348
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.940870
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.492624
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.597075
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.629829
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.315922
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.379814
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.881106
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.851982
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.704846
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.561421
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.491563
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.848827
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.484348
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.940870
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2210.958632
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2283.793432
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.492624
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.597075
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1188.607365
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.014212
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.629829
2 3 4 5 6 7 8
4598 1698 583 157 40 9 3
converting counts to integer mode
Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors
12 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT
[1] 3166
[1] 6967
The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.
groupID featureID featureID.1 groupID.1
8315 ENSG00000253352 ENST00000519077 ENST00000519077.4 ENSG00000253352.10
8316 ENSG00000253352 ENST00000644027 ENST00000644027.1 ENSG00000253352.10
8317 ENSG00000253352 ENST00000644773 ENST00000644773.2 ENSG00000253352.10
6150 ENSG00000173928 ENST00000312423 ENST00000312423.4 ENSG00000173928.4
6151 ENSG00000173928 ENST00000674460 ENST00000674460.1 ENSG00000173928.4
3467 ENSG00000135316 ENST00000355238 ENST00000355238.11 ENSG00000135316.19
gene transcript
8315 0.04979806 0.02006134
8316 0.04979806 0.65219686
8317 0.04979806 1.00000000
6150 0.04972598 0.00000000
6151 0.04972598 0.00000000
3467 0.04966156 1.00000000
gid tid day0.rep1 day0.rep2 day0.rep3
3562 ENSG00000004864.14 ENST00000265631.10 2368.620 1969.083 2190.773
3563 ENSG00000004864.14 ENST00000416240.6 2978.493 2123.488 2322.238
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
3562 2263.717 3309.664 2385.386 2362.016 1885.506 0.000 0.000
3563 2462.271 3309.664 2580.530 2362.016 1885.506 3183.399 3399.719
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
3562 0.000 2978.493 2123.488 2322.238 2462.271 3309.664
3563 2976.813 2368.620 1969.083 2190.773 2263.717 3309.664
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
3562 2580.530 2362.016 1885.506 3183.399
3563 2385.386 2362.016 1885.506 0.000
sample_id day gid tid value
1 day0.rep1 0 ENSG00000004864.14 ENST00000416240.6 2978.493
2 day0.rep1 0 ENSG00000004864.14 ENST00000265631.10 2368.620
3 day0.rep2 0 ENSG00000004864.14 ENST00000265631.10 1969.083
4 day0.rep2 0 ENSG00000004864.14 ENST00000416240.6 2123.488
5 day0.rep3 0 ENSG00000004864.14 ENST00000265631.10 2190.773
6 day0.rep3 0 ENSG00000004864.14 ENST00000416240.6 2322.238
7 day1.rep1 1 ENSG00000004864.14 ENST00000265631.10 2263.717
8 day1.rep1 1 ENSG00000004864.14 ENST00000416240.6 2462.271
9 day2.rep1 2 ENSG00000004864.14 ENST00000265631.10 3309.664
10 day2.rep1 2 ENSG00000004864.14 ENST00000416240.6 3309.664
11 day3.rep1 3 ENSG00000004864.14 ENST00000265631.10 2385.386
12 day3.rep1 3 ENSG00000004864.14 ENST00000416240.6 2580.530
13 day3.rep2 3 ENSG00000004864.14 ENST00000265631.10 2362.016
14 day3.rep2 3 ENSG00000004864.14 ENST00000416240.6 2362.016
15 day4.rep1 4 ENSG00000004864.14 ENST00000416240.6 1885.506
16 day4.rep1 4 ENSG00000004864.14 ENST00000265631.10 1885.506
17 day5.rep1 5 ENSG00000004864.14 ENST00000265631.10 0.000
18 day5.rep1 5 ENSG00000004864.14 ENST00000416240.6 3183.399
19 day5.rep2 5 ENSG00000004864.14 ENST00000416240.6 3399.719
20 day5.rep2 5 ENSG00000004864.14 ENST00000265631.10 0.000
21 day5.rep3 5 ENSG00000004864.14 ENST00000265631.10 0.000
22 day5.rep3 5 ENSG00000004864.14 ENST00000416240.6 2976.813
sample_id day gid tid value
1 day0.rep1 0 ENSG00000004864.14 ENST00000416240.6 2978.493
2 day0.rep1 0 ENSG00000004864.14 ENST00000265631.10 2368.620
3 day0.rep2 0 ENSG00000004864.14 ENST00000265631.10 1969.083
4 day0.rep2 0 ENSG00000004864.14 ENST00000416240.6 2123.488
5 day0.rep3 0 ENSG00000004864.14 ENST00000265631.10 2190.773
6 day0.rep3 0 ENSG00000004864.14 ENST00000416240.6 2322.238
7 day1.rep1 1 ENSG00000004864.14 ENST00000265631.10 2263.717
8 day1.rep1 1 ENSG00000004864.14 ENST00000416240.6 2462.271
9 day2.rep1 2 ENSG00000004864.14 ENST00000265631.10 3309.664
10 day2.rep1 2 ENSG00000004864.14 ENST00000416240.6 3309.664
11 day3.rep1 3 ENSG00000004864.14 ENST00000265631.10 2385.386
12 day3.rep1 3 ENSG00000004864.14 ENST00000416240.6 2580.530
13 day3.rep2 3 ENSG00000004864.14 ENST00000265631.10 2362.016
14 day3.rep2 3 ENSG00000004864.14 ENST00000416240.6 2362.016
15 day4.rep1 4 ENSG00000004864.14 ENST00000416240.6 1885.506
16 day4.rep1 4 ENSG00000004864.14 ENST00000265631.10 1885.506
17 day5.rep1 5 ENSG00000004864.14 ENST00000265631.10 0.000
18 day5.rep1 5 ENSG00000004864.14 ENST00000416240.6 3183.399
19 day5.rep2 5 ENSG00000004864.14 ENST00000416240.6 3399.719
20 day5.rep2 5 ENSG00000004864.14 ENST00000265631.10 0.000
21 day5.rep3 5 ENSG00000004864.14 ENST00000265631.10 0.000
22 day5.rep3 5 ENSG00000004864.14 ENST00000416240.6 2976.813
gid tid day0.rep1 day0.rep2 day0.rep3
3562 ENSG00000004864.14 ENST00000265631.10 2368.620 1969.083 2190.773
3563 ENSG00000004864.14 ENST00000416240.6 2978.493 2123.488 2322.238
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
3562 2263.717 3309.664 2385.386 2362.016 1885.506 0.000 0.000
3563 2462.271 3309.664 2580.530 2362.016 1885.506 3183.399 3399.719
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
3562 0.000 2978.493 2123.488 2322.238 2462.271 3309.664
3563 2976.813 2368.620 1969.083 2190.773 2263.717 3309.664
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
3562 2580.530 2362.016 1885.506 3183.399
3563 2385.386 2362.016 1885.506 0.000
sample_id day gid tid value
1 day0.rep1 0 ENSG00000004864.14 ENST00000416240.6 2978.493
2 day0.rep1 0 ENSG00000004864.14 ENST00000265631.10 2368.620
3 day0.rep2 0 ENSG00000004864.14 ENST00000265631.10 1969.083
4 day0.rep2 0 ENSG00000004864.14 ENST00000416240.6 2123.488
5 day0.rep3 0 ENSG00000004864.14 ENST00000265631.10 2190.773
6 day0.rep3 0 ENSG00000004864.14 ENST00000416240.6 2322.238
7 day1.rep1 1 ENSG00000004864.14 ENST00000265631.10 2263.717
8 day1.rep1 1 ENSG00000004864.14 ENST00000416240.6 2462.271
9 day2.rep1 2 ENSG00000004864.14 ENST00000265631.10 3309.664
10 day2.rep1 2 ENSG00000004864.14 ENST00000416240.6 3309.664
11 day3.rep1 3 ENSG00000004864.14 ENST00000265631.10 2385.386
12 day3.rep1 3 ENSG00000004864.14 ENST00000416240.6 2580.530
13 day3.rep2 3 ENSG00000004864.14 ENST00000265631.10 2362.016
14 day3.rep2 3 ENSG00000004864.14 ENST00000416240.6 2362.016
15 day4.rep1 4 ENSG00000004864.14 ENST00000416240.6 1885.506
16 day4.rep1 4 ENSG00000004864.14 ENST00000265631.10 1885.506
17 day5.rep1 5 ENSG00000004864.14 ENST00000265631.10 0.000
18 day5.rep1 5 ENSG00000004864.14 ENST00000416240.6 3183.399
19 day5.rep2 5 ENSG00000004864.14 ENST00000416240.6 3399.719
20 day5.rep2 5 ENSG00000004864.14 ENST00000265631.10 0.000
21 day5.rep3 5 ENSG00000004864.14 ENST00000265631.10 0.000
22 day5.rep3 5 ENSG00000004864.14 ENST00000416240.6 2976.813
sample_id day gid tid value
1 day0.rep1 0 ENSG00000004864.14 ENST00000416240.6 2978.493
2 day0.rep1 0 ENSG00000004864.14 ENST00000265631.10 2368.620
3 day0.rep2 0 ENSG00000004864.14 ENST00000265631.10 1969.083
4 day0.rep2 0 ENSG00000004864.14 ENST00000416240.6 2123.488
5 day0.rep3 0 ENSG00000004864.14 ENST00000265631.10 2190.773
6 day0.rep3 0 ENSG00000004864.14 ENST00000416240.6 2322.238
7 day1.rep1 1 ENSG00000004864.14 ENST00000265631.10 2263.717
8 day1.rep1 1 ENSG00000004864.14 ENST00000416240.6 2462.271
9 day2.rep1 2 ENSG00000004864.14 ENST00000265631.10 3309.664
10 day2.rep1 2 ENSG00000004864.14 ENST00000416240.6 3309.664
11 day3.rep1 3 ENSG00000004864.14 ENST00000265631.10 2385.386
12 day3.rep1 3 ENSG00000004864.14 ENST00000416240.6 2580.530
13 day3.rep2 3 ENSG00000004864.14 ENST00000265631.10 2362.016
14 day3.rep2 3 ENSG00000004864.14 ENST00000416240.6 2362.016
15 day4.rep1 4 ENSG00000004864.14 ENST00000416240.6 1885.506
16 day4.rep1 4 ENSG00000004864.14 ENST00000265631.10 1885.506
17 day5.rep1 5 ENSG00000004864.14 ENST00000265631.10 0.000
18 day5.rep1 5 ENSG00000004864.14 ENST00000416240.6 3183.399
19 day5.rep2 5 ENSG00000004864.14 ENST00000416240.6 3399.719
20 day5.rep2 5 ENSG00000004864.14 ENST00000265631.10 0.000
21 day5.rep3 5 ENSG00000004864.14 ENST00000265631.10 0.000
22 day5.rep3 5 ENSG00000004864.14 ENST00000416240.6 2976.813
confirmed_salmon_0.025 <- res_salmon_0.025[res_salmon_0.025$transcript < 0.05, ]
nrow(confirmed_salmon_0.025)[1] 2358
confirmed_bambu_0.025 <- res_bambu_0.025[res_bambu_0.025$transcript < 0.05, ]
nrow(confirmed_bambu_0.025)[1] 6316
For Illumina+Salmon, out of the 9901 tested genes and 27084 tested features, DEXSeq test identified 1457 genes showing evidence of isoform switching involving 2409 transcripts. For PacBio+Bambu out of the 7088 tested genes and 17734 tested features, 3166 genes involving 6967 trancsripts were identified.
After the stageR procedure, 2358 transcripts passed the confirmation stage for Illumina+Salmon and 6316 transcripts for PacBio+Bambu on a target 5% overall false discovery rate (OFDR). This means that, in expectation, no more than 5% of the genes that pass screening will either (1) not contain any DTU, so be falsely screened genes, or (2) contain a falsely confirmed transcript.
Upset Plot
[1] 742
venn <- list(SALMON = confirmed_salmon_0.025$GeneID, BAMBU = confirmed_bambu_0.025$GeneID)
ggvenn(venn)# Confirmed Transcripts
length(intersect(confirmed_salmon_0.025$TranscriptID, confirmed_bambu_0.025$TranscriptID))[1] 834
venn <- list(SALMON = confirmed_salmon_0.025$TranscriptID, BAMBU = confirmed_bambu_0.025$TranscriptID)
ggvenn(venn)From the UpSet plot and Venn Diagram above it is visible that through PacBio+Bambu many more transcripts were detected through DTU. The overlap between Illumina+Salmon was also only roughly 11 %.
Comparsion of pAdj and logFC
both_detected <-
intersect(res_bambu_0.025$TranscriptID, res_salmon_0.025$TranscriptID)
sorted_res_salmon_0.025 <- res_salmon_0.025[order(res_salmon_0.025$TranscriptID),]
both_sorted_res_salmon_0.025 <- sorted_res_salmon_0.025[which(sorted_res_salmon_0.025$TranscriptID %in% both_detected), ]
sorted_res_bambu_0.025 <- res_bambu_0.025[order(res_bambu_0.025$TranscriptID),]
both_sorted_res_bambu_0.025 <- sorted_res_bambu_0.025[which(sorted_res_bambu_0.025$TranscriptID %in% both_detected), ]
padj <- data.frame(Salmon = both_sorted_res_salmon_0.025$transcript, Bambu = both_sorted_res_bambu_0.025$transcript)
ggplot(data = padj, mapping = aes(x = -log10(Salmon), y = -log10(Bambu))) +
geom_point() +
geom_smooth() +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
scale_color_viridis() +
labs(title = "Comparison of P-values (NDR=0.025)", x = "-log10 P-value (Salmon)", y = "-log10 P-value (Bambu)")`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'
Warning: Removed 663 rows containing non-finite values (`stat_smooth()`).
logfc <- data.frame(Salmon = both_sorted_res_salmon_0.025$log2fc, Bambu = both_sorted_res_bambu_0.025$log2fc)
ggplot(data = logfc, mapping = aes(x = Salmon, y = Bambu)) +
geom_point() +
geom_smooth() +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
scale_color_viridis() +
labs(title = "Comparison of LogFC (NDR=0.025)", x = "LogFC (Salmon)", y = "LogFC (Bambu)")`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'
The comparison of the adjusted p-values for transcripts shows low correlation between technologies especially for higher values. The logFC values seem to be, however, better correlated with some deviations for the extreme values.
NDR 0.05
# Transcript to gene mappings
txdf <- df_list_meta$metagenes_0.05
res_salmon_0.05 <- DTU(salmon_0.05, txdf, "salmon_0.05.", n = 3, n.small = 3)
2 3 4 5 6 7 8 9
5251 2903 1216 434 114 29 8 3
converting counts to integer mode
Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors
32 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT
[1] 1468
[1] 2436
The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.
groupID featureID featureID.1 groupID.1
95 ENSG00000010626 ENST00000007969 ENST00000007969.12 ENSG00000010626.15
96 ENSG00000010626 ENST00000323702 ENST00000323702.9 ENSG00000010626.15
97 ENSG00000010626 ENST00000428946 ENST00000428946.5 ENSG00000010626.15
98 ENSG00000010626 ENST00000433346 ENST00000433346.5 ENSG00000010626.15
99 ENSG00000010626 ENST00000451681 ENST00000451681.5 ENSG00000010626.15
4244 ENSG00000205571 ENST00000380743 ENST00000380743.9 ENSG00000205571.14
gene transcript
95 0.04990835 0.05492203
96 0.04990835 1.00000000
97 0.04990835 0.93057242
98 0.04990835 1.00000000
99 0.04990835 1.00000000
4244 0.04987648 0.38058073
gid tid day0.rep1 day0.rep2 day0.rep3
11192 ENSG00000010671.17 ENST00000308731.8 0.00000 0.00000 0.00000
11193 ENSG00000010671.17 ENST00000621635.4 34.30906 18.37431 21.88094
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
11192 3.85061 62.5304 915.4657 849.401157 2210.68147 2283.87095 1189.58092
11193 33.69284 0.0000 0.0000 8.479878 57.93361 28.49359 46.63524
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
11192 1114.45344 34.30906 18.37431 21.88094 33.69284 0.0000
11193 41.64624 0.00000 0.00000 0.00000 3.85061 62.5304
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
11192 0.0000 8.479878 57.93361 28.49359
11193 915.4657 849.401157 2210.68147 2283.87095
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.309065
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.374312
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.880936
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.850610
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.692839
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.530403
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.465737
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.401157
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.479878
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.933607
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2210.681474
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2283.870953
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.493592
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.635242
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1189.580924
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.453441
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.646242
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.309065
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.374312
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.880936
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.850610
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.692839
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.530403
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.465737
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.401157
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.479878
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.933607
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2210.681474
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2283.870953
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.493592
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.635242
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1189.580924
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.453441
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.646242
gid tid day0.rep1 day0.rep2 day0.rep3
11192 ENSG00000010671.17 ENST00000308731.8 0.00000 0.00000 0.00000
11193 ENSG00000010671.17 ENST00000621635.4 34.30906 18.37431 21.88094
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
11192 3.85061 62.5304 915.4657 849.401157 2210.68147 2283.87095 1189.58092
11193 33.69284 0.0000 0.0000 8.479878 57.93361 28.49359 46.63524
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
11192 1114.45344 34.30906 18.37431 21.88094 33.69284 0.0000
11193 41.64624 0.00000 0.00000 0.00000 3.85061 62.5304
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
11192 0.0000 8.479878 57.93361 28.49359
11193 915.4657 849.401157 2210.68147 2283.87095
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.309065
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.374312
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.880936
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.850610
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.692839
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.530403
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.465737
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.401157
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.479878
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.933607
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2210.681474
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2283.870953
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.493592
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.635242
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1189.580924
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.453441
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.646242
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.309065
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.374312
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.880936
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.850610
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.692839
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.530403
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.465737
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.401157
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.479878
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.933607
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2210.681474
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2283.870953
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.493592
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.635242
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1189.580924
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.453441
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.646242
2 3 4 5 6 7 8
4650 1715 593 161 40 9 3
converting counts to integer mode
Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors
10 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT
[1] 3217
[1] 7087
The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.
groupID featureID featureID.1 groupID.1
7936 ENSG00000215252 ENST00000342314 ENST00000342314.9 ENSG00000215252.12
7937 ENSG00000215252 ENST00000484716 ENST00000484716.5 ENSG00000215252.12
7938 ENSG00000215252 ENST00000569100 ENST00000569100.5 ENSG00000215252.12
7939 ENSG00000215252 ENST00000683415 ENST00000683415.1 ENSG00000215252.12
8349 ENSG00000245275 ENST00000501280 ENST00000501280.4 ENSG00000245275.8
8350 ENSG00000245275 ENST00000522312 ENST00000522312.1 ENSG00000245275.8
gene transcript
7936 0.04996308 0.0402418
7937 0.04996308 0.2496524
7938 0.04996308 1.0000000
7939 0.04996308 0.1464222
8349 0.04910182 0.0000000
8350 0.04910182 0.0000000
gid tid day0.rep1 day0.rep2 day0.rep3 day1.rep1 day2.rep1
484 BambuGene96616 BambuTx435 2.793872 6.77563 12.84754 2.946682 44.86370
485 BambuGene96616 BambuTx470 42.839368 103.32836 85.34439 21.608999 24.15738
day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2 day5.rep3
484 487.199975 952.8257672 1252.7550454 5768.24595 5685.838667 3370.87261
485 1.282105 0.9537795 0.9012626 1.03522 3.170689 4.08096
day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1 day3.rep1.1
484 42.839368 103.32836 85.34439 21.608999 24.15738 1.282105
485 2.793872 6.77563 12.84754 2.946682 44.86370 487.199975
day3.rep2.1 day4.rep1.1 day5.rep1.1
484 0.9537795 0.9012626 1.03522
485 952.8257672 1252.7550454 5768.24595
sample_id day gid tid value
1 day0.rep1 0 BambuGene96616 BambuTx470 42.8393679
2 day0.rep1 0 BambuGene96616 BambuTx435 2.7938718
3 day0.rep2 0 BambuGene96616 BambuTx435 6.7756300
4 day0.rep2 0 BambuGene96616 BambuTx470 103.3283572
5 day0.rep3 0 BambuGene96616 BambuTx435 12.8475432
6 day0.rep3 0 BambuGene96616 BambuTx470 85.3443940
7 day1.rep1 1 BambuGene96616 BambuTx435 2.9466817
8 day1.rep1 1 BambuGene96616 BambuTx470 21.6089989
9 day2.rep1 2 BambuGene96616 BambuTx435 44.8637024
10 day2.rep1 2 BambuGene96616 BambuTx470 24.1573782
11 day3.rep1 3 BambuGene96616 BambuTx435 487.1999748
12 day3.rep1 3 BambuGene96616 BambuTx470 1.2821052
13 day3.rep2 3 BambuGene96616 BambuTx435 952.8257672
14 day3.rep2 3 BambuGene96616 BambuTx470 0.9537795
15 day4.rep1 4 BambuGene96616 BambuTx470 0.9012626
16 day4.rep1 4 BambuGene96616 BambuTx435 1252.7550454
17 day5.rep1 5 BambuGene96616 BambuTx435 5768.2459491
18 day5.rep1 5 BambuGene96616 BambuTx470 1.0352200
19 day5.rep2 5 BambuGene96616 BambuTx470 3.1706893
20 day5.rep2 5 BambuGene96616 BambuTx435 5685.8386674
21 day5.rep3 5 BambuGene96616 BambuTx435 3370.8726078
22 day5.rep3 5 BambuGene96616 BambuTx470 4.0809596
sample_id day gid tid value
1 day0.rep1 0 BambuGene96616 BambuTx470 42.8393679
2 day0.rep1 0 BambuGene96616 BambuTx435 2.7938718
3 day0.rep2 0 BambuGene96616 BambuTx435 6.7756300
4 day0.rep2 0 BambuGene96616 BambuTx470 103.3283572
5 day0.rep3 0 BambuGene96616 BambuTx435 12.8475432
6 day0.rep3 0 BambuGene96616 BambuTx470 85.3443940
7 day1.rep1 1 BambuGene96616 BambuTx435 2.9466817
8 day1.rep1 1 BambuGene96616 BambuTx470 21.6089989
9 day2.rep1 2 BambuGene96616 BambuTx435 44.8637024
10 day2.rep1 2 BambuGene96616 BambuTx470 24.1573782
11 day3.rep1 3 BambuGene96616 BambuTx435 487.1999748
12 day3.rep1 3 BambuGene96616 BambuTx470 1.2821052
13 day3.rep2 3 BambuGene96616 BambuTx435 952.8257672
14 day3.rep2 3 BambuGene96616 BambuTx470 0.9537795
15 day4.rep1 4 BambuGene96616 BambuTx470 0.9012626
16 day4.rep1 4 BambuGene96616 BambuTx435 1252.7550454
17 day5.rep1 5 BambuGene96616 BambuTx435 5768.2459491
18 day5.rep1 5 BambuGene96616 BambuTx470 1.0352200
19 day5.rep2 5 BambuGene96616 BambuTx470 3.1706893
20 day5.rep2 5 BambuGene96616 BambuTx435 5685.8386674
21 day5.rep3 5 BambuGene96616 BambuTx435 3370.8726078
22 day5.rep3 5 BambuGene96616 BambuTx470 4.0809596
gid tid day0.rep1 day0.rep2 day0.rep3 day1.rep1 day2.rep1
484 BambuGene96616 BambuTx435 2.793872 6.77563 12.84754 2.946682 44.86370
485 BambuGene96616 BambuTx470 42.839368 103.32836 85.34439 21.608999 24.15738
day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2 day5.rep3
484 487.199975 952.8257672 1252.7550454 5768.24595 5685.838667 3370.87261
485 1.282105 0.9537795 0.9012626 1.03522 3.170689 4.08096
day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1 day3.rep1.1
484 42.839368 103.32836 85.34439 21.608999 24.15738 1.282105
485 2.793872 6.77563 12.84754 2.946682 44.86370 487.199975
day3.rep2.1 day4.rep1.1 day5.rep1.1
484 0.9537795 0.9012626 1.03522
485 952.8257672 1252.7550454 5768.24595
sample_id day gid tid value
1 day0.rep1 0 BambuGene96616 BambuTx470 42.8393679
2 day0.rep1 0 BambuGene96616 BambuTx435 2.7938718
3 day0.rep2 0 BambuGene96616 BambuTx435 6.7756300
4 day0.rep2 0 BambuGene96616 BambuTx470 103.3283572
5 day0.rep3 0 BambuGene96616 BambuTx435 12.8475432
6 day0.rep3 0 BambuGene96616 BambuTx470 85.3443940
7 day1.rep1 1 BambuGene96616 BambuTx435 2.9466817
8 day1.rep1 1 BambuGene96616 BambuTx470 21.6089989
9 day2.rep1 2 BambuGene96616 BambuTx435 44.8637024
10 day2.rep1 2 BambuGene96616 BambuTx470 24.1573782
11 day3.rep1 3 BambuGene96616 BambuTx435 487.1999748
12 day3.rep1 3 BambuGene96616 BambuTx470 1.2821052
13 day3.rep2 3 BambuGene96616 BambuTx435 952.8257672
14 day3.rep2 3 BambuGene96616 BambuTx470 0.9537795
15 day4.rep1 4 BambuGene96616 BambuTx470 0.9012626
16 day4.rep1 4 BambuGene96616 BambuTx435 1252.7550454
17 day5.rep1 5 BambuGene96616 BambuTx435 5768.2459491
18 day5.rep1 5 BambuGene96616 BambuTx470 1.0352200
19 day5.rep2 5 BambuGene96616 BambuTx470 3.1706893
20 day5.rep2 5 BambuGene96616 BambuTx435 5685.8386674
21 day5.rep3 5 BambuGene96616 BambuTx435 3370.8726078
22 day5.rep3 5 BambuGene96616 BambuTx470 4.0809596
sample_id day gid tid value
1 day0.rep1 0 BambuGene96616 BambuTx470 42.8393679
2 day0.rep1 0 BambuGene96616 BambuTx435 2.7938718
3 day0.rep2 0 BambuGene96616 BambuTx435 6.7756300
4 day0.rep2 0 BambuGene96616 BambuTx470 103.3283572
5 day0.rep3 0 BambuGene96616 BambuTx435 12.8475432
6 day0.rep3 0 BambuGene96616 BambuTx470 85.3443940
7 day1.rep1 1 BambuGene96616 BambuTx435 2.9466817
8 day1.rep1 1 BambuGene96616 BambuTx470 21.6089989
9 day2.rep1 2 BambuGene96616 BambuTx435 44.8637024
10 day2.rep1 2 BambuGene96616 BambuTx470 24.1573782
11 day3.rep1 3 BambuGene96616 BambuTx435 487.1999748
12 day3.rep1 3 BambuGene96616 BambuTx470 1.2821052
13 day3.rep2 3 BambuGene96616 BambuTx435 952.8257672
14 day3.rep2 3 BambuGene96616 BambuTx470 0.9537795
15 day4.rep1 4 BambuGene96616 BambuTx470 0.9012626
16 day4.rep1 4 BambuGene96616 BambuTx435 1252.7550454
17 day5.rep1 5 BambuGene96616 BambuTx435 5768.2459491
18 day5.rep1 5 BambuGene96616 BambuTx470 1.0352200
19 day5.rep2 5 BambuGene96616 BambuTx470 3.1706893
20 day5.rep2 5 BambuGene96616 BambuTx435 5685.8386674
21 day5.rep3 5 BambuGene96616 BambuTx435 3370.8726078
22 day5.rep3 5 BambuGene96616 BambuTx470 4.0809596
confirmed_salmon_0.05 <- res_salmon_0.05[res_salmon_0.05$transcript < 0.05, ]
nrow(confirmed_salmon_0.05)[1] 2375
confirmed_bambu_0.05 <- res_bambu_0.05[res_bambu_0.05$transcript < 0.05, ]
nrow(confirmed_bambu_0.05)[1] 6427
For Illumina+Salmon, out of the 9958 tested genes and 27223 tested features, DEXSeq test identified 1468 genes showing evidence of isoform switching involving 2436 transcripts. For PacBio+Bambu out of the 7171 tested genes and 17949 tested features, 3217 genes involving 7087 trancsripts were identified.
After the stageR procedure, 2375 transcripts passed the confirmation stage for Illumina+Salmon and 6427 transcripts for PacBio+Bambu on a target 5% overall false discovery rate (OFDR). This means that, in expectation, no more than 5% of the genes that pass screening will either (1) not contain any DTU, so be falsely screened genes, or (2) contain a falsely confirmed transcript.
Upset Plot
[1] 752
venn <- list(SALMON = confirmed_salmon_0.05$GeneID, BAMBU = confirmed_bambu_0.05$GeneID)
ggvenn(venn)# Confirmed Transcripts
length(intersect(confirmed_salmon_0.05$TranscriptID, confirmed_bambu_0.05$TranscriptID))[1] 844
venn <- list(SALMON = confirmed_salmon_0.05$TranscriptID, BAMBU = confirmed_bambu_0.05$TranscriptID)
ggvenn(venn)From the UpSet plot and Venn Diagram above it is visible that through PacBio+Bambu many more transcripts were detected through DTU. The overlap between Illumina+Salmon was also only roughly 11 %.
Comparsion of pAdj and logFC
both_detected <-
intersect(res_bambu_0.05$TranscriptID, res_salmon_0.05$TranscriptID)
sorted_res_salmon_0.05 <- res_salmon_0.05[order(res_salmon_0.05$TranscriptID),]
both_sorted_res_salmon_0.05 <- sorted_res_salmon_0.05[which(sorted_res_salmon_0.05$TranscriptID %in% both_detected), ]
sorted_res_bambu_0.05 <- res_bambu_0.05[order(res_bambu_0.05$TranscriptID),]
both_sorted_res_bambu_0.05 <- sorted_res_bambu_0.05[which(sorted_res_bambu_0.05$TranscriptID %in% both_detected), ]
padj <- data.frame(Salmon = both_sorted_res_salmon_0.05$transcript, Bambu = both_sorted_res_bambu_0.05$transcript)
ggplot(data = padj, mapping = aes(x = -log10(Salmon), y = -log10(Bambu))) +
geom_point() +
geom_smooth() +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
scale_color_viridis() +
labs(title = "Comparison of P-values (NDR=0.05)", x = "-log10 P-value (Salmon)", y = "-log10 P-value (Bambu)")`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'
Warning: Removed 667 rows containing non-finite values (`stat_smooth()`).
logfc <- data.frame(Salmon = both_sorted_res_salmon_0.05$log2fc, Bambu = both_sorted_res_bambu_0.05$log2fc)
ggplot(data = logfc, mapping = aes(x = Salmon, y = Bambu)) +
geom_point() +
geom_smooth() +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
scale_color_viridis() +
labs(title = "Comparison of LogFC (NDR=0.05)", x = "LogFC (Salmon)", y = "LogFC (Bambu)")`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'
The comparison of the adjusted p-values for transcripts shows low correlation between technologies especially for higher values. The logFC values seem to be, however, better correlated with some deviations for the extreme values.
NDR 0.1
# Transcript to gene mappings
txdf <- df_list_meta$metagenes_0.1
res_salmon_0.1 <- DTU(salmon_0.1, txdf, "salmon_0.1.", n = 3, n.small = 3)
2 3 4 5 6 7 8 9
5292 2929 1228 448 116 28 8 3
converting counts to integer mode
Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors
27 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT
[1] 1507
[1] 2505
The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.
groupID featureID featureID.1 groupID.1
1799 ENSG00000130714 ENST00000341012 ENST00000341012.13 ENSG00000130714.19
1800 ENSG00000130714 ENST00000402686 ENST00000402686.8 ENSG00000130714.19
1801 ENSG00000130714 ENST00000683392 ENST00000683392.1 ENSG00000130714.19
4555 ENSG00000233822 ENST00000606613 ENST00000606613.1 ENSG00000233822.6
4556 ENSG00000233822 ENST00000612898 ENST00000612898.2 ENSG00000233822.6
3696 ENSG00000175287 ENST00000308941 ENST00000308941.9 ENSG00000175287.19
gene transcript
1799 0.04974351 1.00000000
1800 0.04974351 1.00000000
1801 0.04974351 0.01820608
4555 0.04973010 0.00000000
4556 0.04973010 0.00000000
3696 0.04972740 1.00000000
gid tid day0.rep1 day0.rep2 day0.rep3
11897 ENSG00000010671.17 ENST00000308731.8 0.00000 0.00000 0.00000
11898 ENSG00000010671.17 ENST00000621635.4 34.30906 18.38182 21.87258
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
11897 3.848584 62.53679 915.4419 849.164288 2211.61114 2285.02984 1189.65518
11898 33.675107 0.00000 0.0000 8.477514 57.95797 28.50805 46.63815
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
11897 1114.87293 34.30906 18.38182 21.87258 33.675107 0.00000
11898 41.66192 0.00000 0.00000 0.00000 3.848584 62.53679
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
11897 0.0000 8.477514 57.95797 28.50805
11898 915.4419 849.164288 2211.61114 2285.02984
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.309065
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.381821
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.872575
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.848584
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.675107
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.536788
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.441938
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.164288
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.477514
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.957970
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2211.611137
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2285.029844
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.508050
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.638153
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1189.655176
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.872926
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.661918
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.309065
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.381821
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.872575
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.848584
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.675107
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.536788
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.441938
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.164288
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.477514
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.957970
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2211.611137
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2285.029844
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.508050
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.638153
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1189.655176
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.872926
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.661918
gid tid day0.rep1 day0.rep2 day0.rep3
11897 ENSG00000010671.17 ENST00000308731.8 0.00000 0.00000 0.00000
11898 ENSG00000010671.17 ENST00000621635.4 34.30906 18.38182 21.87258
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
11897 3.848584 62.53679 915.4419 849.164288 2211.61114 2285.02984 1189.65518
11898 33.675107 0.00000 0.0000 8.477514 57.95797 28.50805 46.63815
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
11897 1114.87293 34.30906 18.38182 21.87258 33.675107 0.00000
11898 41.66192 0.00000 0.00000 0.00000 3.848584 62.53679
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
11897 0.0000 8.477514 57.95797 28.50805
11898 915.4419 849.164288 2211.61114 2285.02984
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.309065
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.381821
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.872575
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.848584
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.675107
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.536788
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.441938
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.164288
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.477514
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.957970
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2211.611137
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2285.029844
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.508050
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.638153
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1189.655176
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.872926
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.661918
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.309065
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.381821
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.872575
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.848584
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.675107
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.536788
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 915.441938
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 849.164288
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.477514
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.957970
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2211.611137
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2285.029844
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.508050
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.638153
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1189.655176
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.872926
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.661918
2 3 4 5 6 7 8
4767 1774 610 163 41 8 3
converting counts to integer mode
Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors
9 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT
[1] 3316
[1] 7332
The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.
groupID featureID featureID.1 groupID.1
3089 ENSG00000128487 ENST00000395530 ENST00000395530.6 ENSG00000128487.19
3090 ENSG00000128487 ENST00000581399 ENST00000581399.6 ENSG00000128487.19
4725 ENSG00000151806 BambuTx299 BambuTx299 ENSG00000151806.14
4726 ENSG00000151806 ENST00000281543 ENST00000281543.6 ENSG00000151806.14
4670 ENSG00000150672 ENST00000376104 ENST00000376104.7 ENSG00000150672.18
4671 ENSG00000150672 ENST00000398309 ENST00000398309.6 ENSG00000150672.18
gene transcript
3089 0.04996015 0.0000000
3090 0.04996015 0.0000000
4725 0.04972857 0.0000000
4726 0.04972857 0.0000000
4670 0.04953250 0.8551188
4671 0.04953250 0.8294748
gid tid day0.rep1 day0.rep2 day0.rep3 day1.rep1
233 BambuGene96616 BambuTx1180 2.785771 6.775579 12.84737 2.945325
234 BambuGene96616 BambuTx1181 42.715158 103.327582 85.34327 21.599052
day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
233 45.25648 485.459573 954.2535645 1252.4865423 5764.766530 5691.780908
234 24.36887 1.277525 0.9552088 0.9010695 1.034596 3.174003
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
233 3358.146591 42.715158 103.327582 85.34327 21.599052 24.36887
234 4.065553 2.785771 6.775579 12.84737 2.945325 45.25648
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
233 1.277525 0.9552088 0.9010695 1.034596
234 485.459573 954.2535645 1252.4865423 5764.766530
sample_id day gid tid value
1 day0.rep1 0 BambuGene96616 BambuTx1181 42.7151581
2 day0.rep1 0 BambuGene96616 BambuTx1180 2.7857712
3 day0.rep2 0 BambuGene96616 BambuTx1180 6.7755791
4 day0.rep2 0 BambuGene96616 BambuTx1181 103.3275817
5 day0.rep3 0 BambuGene96616 BambuTx1180 12.8473740
6 day0.rep3 0 BambuGene96616 BambuTx1181 85.3432698
7 day1.rep1 1 BambuGene96616 BambuTx1180 2.9453252
8 day1.rep1 1 BambuGene96616 BambuTx1181 21.5990517
9 day2.rep1 2 BambuGene96616 BambuTx1180 45.2564765
10 day2.rep1 2 BambuGene96616 BambuTx1181 24.3688720
11 day3.rep1 3 BambuGene96616 BambuTx1180 485.4595730
12 day3.rep1 3 BambuGene96616 BambuTx1181 1.2775252
13 day3.rep2 3 BambuGene96616 BambuTx1180 954.2535645
14 day3.rep2 3 BambuGene96616 BambuTx1181 0.9552088
15 day4.rep1 4 BambuGene96616 BambuTx1181 0.9010695
16 day4.rep1 4 BambuGene96616 BambuTx1180 1252.4865423
17 day5.rep1 5 BambuGene96616 BambuTx1180 5764.7665301
18 day5.rep1 5 BambuGene96616 BambuTx1181 1.0345956
19 day5.rep2 5 BambuGene96616 BambuTx1181 3.1740030
20 day5.rep2 5 BambuGene96616 BambuTx1180 5691.7809077
21 day5.rep3 5 BambuGene96616 BambuTx1180 3358.1465912
22 day5.rep3 5 BambuGene96616 BambuTx1181 4.0655528
sample_id day gid tid value
1 day0.rep1 0 BambuGene96616 BambuTx1181 42.7151581
2 day0.rep1 0 BambuGene96616 BambuTx1180 2.7857712
3 day0.rep2 0 BambuGene96616 BambuTx1180 6.7755791
4 day0.rep2 0 BambuGene96616 BambuTx1181 103.3275817
5 day0.rep3 0 BambuGene96616 BambuTx1180 12.8473740
6 day0.rep3 0 BambuGene96616 BambuTx1181 85.3432698
7 day1.rep1 1 BambuGene96616 BambuTx1180 2.9453252
8 day1.rep1 1 BambuGene96616 BambuTx1181 21.5990517
9 day2.rep1 2 BambuGene96616 BambuTx1180 45.2564765
10 day2.rep1 2 BambuGene96616 BambuTx1181 24.3688720
11 day3.rep1 3 BambuGene96616 BambuTx1180 485.4595730
12 day3.rep1 3 BambuGene96616 BambuTx1181 1.2775252
13 day3.rep2 3 BambuGene96616 BambuTx1180 954.2535645
14 day3.rep2 3 BambuGene96616 BambuTx1181 0.9552088
15 day4.rep1 4 BambuGene96616 BambuTx1181 0.9010695
16 day4.rep1 4 BambuGene96616 BambuTx1180 1252.4865423
17 day5.rep1 5 BambuGene96616 BambuTx1180 5764.7665301
18 day5.rep1 5 BambuGene96616 BambuTx1181 1.0345956
19 day5.rep2 5 BambuGene96616 BambuTx1181 3.1740030
20 day5.rep2 5 BambuGene96616 BambuTx1180 5691.7809077
21 day5.rep3 5 BambuGene96616 BambuTx1180 3358.1465912
22 day5.rep3 5 BambuGene96616 BambuTx1181 4.0655528
gid tid day0.rep1 day0.rep2 day0.rep3 day1.rep1
233 BambuGene96616 BambuTx1180 2.785771 6.775579 12.84737 2.945325
234 BambuGene96616 BambuTx1181 42.715158 103.327582 85.34327 21.599052
day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
233 45.25648 485.459573 954.2535645 1252.4865423 5764.766530 5691.780908
234 24.36887 1.277525 0.9552088 0.9010695 1.034596 3.174003
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
233 3358.146591 42.715158 103.327582 85.34327 21.599052 24.36887
234 4.065553 2.785771 6.775579 12.84737 2.945325 45.25648
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
233 1.277525 0.9552088 0.9010695 1.034596
234 485.459573 954.2535645 1252.4865423 5764.766530
sample_id day gid tid value
1 day0.rep1 0 BambuGene96616 BambuTx1181 42.7151581
2 day0.rep1 0 BambuGene96616 BambuTx1180 2.7857712
3 day0.rep2 0 BambuGene96616 BambuTx1180 6.7755791
4 day0.rep2 0 BambuGene96616 BambuTx1181 103.3275817
5 day0.rep3 0 BambuGene96616 BambuTx1180 12.8473740
6 day0.rep3 0 BambuGene96616 BambuTx1181 85.3432698
7 day1.rep1 1 BambuGene96616 BambuTx1180 2.9453252
8 day1.rep1 1 BambuGene96616 BambuTx1181 21.5990517
9 day2.rep1 2 BambuGene96616 BambuTx1180 45.2564765
10 day2.rep1 2 BambuGene96616 BambuTx1181 24.3688720
11 day3.rep1 3 BambuGene96616 BambuTx1180 485.4595730
12 day3.rep1 3 BambuGene96616 BambuTx1181 1.2775252
13 day3.rep2 3 BambuGene96616 BambuTx1180 954.2535645
14 day3.rep2 3 BambuGene96616 BambuTx1181 0.9552088
15 day4.rep1 4 BambuGene96616 BambuTx1181 0.9010695
16 day4.rep1 4 BambuGene96616 BambuTx1180 1252.4865423
17 day5.rep1 5 BambuGene96616 BambuTx1180 5764.7665301
18 day5.rep1 5 BambuGene96616 BambuTx1181 1.0345956
19 day5.rep2 5 BambuGene96616 BambuTx1181 3.1740030
20 day5.rep2 5 BambuGene96616 BambuTx1180 5691.7809077
21 day5.rep3 5 BambuGene96616 BambuTx1180 3358.1465912
22 day5.rep3 5 BambuGene96616 BambuTx1181 4.0655528
sample_id day gid tid value
1 day0.rep1 0 BambuGene96616 BambuTx1181 42.7151581
2 day0.rep1 0 BambuGene96616 BambuTx1180 2.7857712
3 day0.rep2 0 BambuGene96616 BambuTx1180 6.7755791
4 day0.rep2 0 BambuGene96616 BambuTx1181 103.3275817
5 day0.rep3 0 BambuGene96616 BambuTx1180 12.8473740
6 day0.rep3 0 BambuGene96616 BambuTx1181 85.3432698
7 day1.rep1 1 BambuGene96616 BambuTx1180 2.9453252
8 day1.rep1 1 BambuGene96616 BambuTx1181 21.5990517
9 day2.rep1 2 BambuGene96616 BambuTx1180 45.2564765
10 day2.rep1 2 BambuGene96616 BambuTx1181 24.3688720
11 day3.rep1 3 BambuGene96616 BambuTx1180 485.4595730
12 day3.rep1 3 BambuGene96616 BambuTx1181 1.2775252
13 day3.rep2 3 BambuGene96616 BambuTx1180 954.2535645
14 day3.rep2 3 BambuGene96616 BambuTx1181 0.9552088
15 day4.rep1 4 BambuGene96616 BambuTx1181 0.9010695
16 day4.rep1 4 BambuGene96616 BambuTx1180 1252.4865423
17 day5.rep1 5 BambuGene96616 BambuTx1180 5764.7665301
18 day5.rep1 5 BambuGene96616 BambuTx1181 1.0345956
19 day5.rep2 5 BambuGene96616 BambuTx1181 3.1740030
20 day5.rep2 5 BambuGene96616 BambuTx1180 5691.7809077
21 day5.rep3 5 BambuGene96616 BambuTx1180 3358.1465912
22 day5.rep3 5 BambuGene96616 BambuTx1181 4.0655528
confirmed_salmon_0.1 <- res_salmon_0.1[res_salmon_0.1$transcript < 0.05, ]
nrow(confirmed_salmon_0.1)[1] 2430
[1] 6661
For Illumina+Salmon, out of the 10052 tested genes and 27506 tested features, DEXSeq test identified 1507 genes showing evidence of isoform switching involving 2505 transcripts. For PacBio+Bambu out of the 7366 tested genes and 18437 tested features, 3316 genes involving 7332 trancsripts were identified.
After the stageR procedure, 2430 transcripts passed the confirmation stage for Illumina+Salmon and 6661 transcripts for PacBio+Bambu on a target 5% overall false discovery rate (OFDR). This means that, in expectation, no more than 5% of the genes that pass screening will either (1) not contain any DTU, so be falsely screened genes, or (2) contain a falsely confirmed transcript.
Upset Plot
[1] 779
# Confirmed Transcripts
length(intersect(confirmed_salmon_0.1$TranscriptID, confirmed_bambu_0.1$TranscriptID))[1] 879
venn <- list(SALMON = confirmed_salmon_0.1$TranscriptID, BAMBU = confirmed_bambu_0.1$TranscriptID)
ggvenn(venn)From the UpSet plot and Venn Diagram above it is visible that through PacBio+Bambu many more transcripts were detected through DTU. The overlap between Illumina+Salmon was also only roughly 11 %.
Comparsion of pAdj and logFC
both_detected <-
intersect(res_bambu_0.1$TranscriptID, res_salmon_0.1$TranscriptID)
sorted_res_salmon_0.1 <- res_salmon_0.1[order(res_salmon_0.1$TranscriptID),]
both_sorted_res_salmon_0.1 <- sorted_res_salmon_0.1[which(sorted_res_salmon_0.1$TranscriptID %in% both_detected), ]
sorted_res_bambu_0.1 <- res_bambu_0.1[order(res_bambu_0.1$TranscriptID),]
both_sorted_res_bambu_0.1 <- sorted_res_bambu_0.1[which(sorted_res_bambu_0.1$TranscriptID %in% both_detected), ]
padj <- data.frame(Salmon = both_sorted_res_salmon_0.1$transcript, Bambu = both_sorted_res_bambu_0.1$transcript)
ggplot(data = padj, mapping = aes(x = -log10(Salmon), y = -log10(Bambu))) +
geom_point() +
geom_smooth() +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
scale_color_viridis() +
labs(title = "Comparison of P-values (NDR=0.1)", x = "-log10 P-value (Salmon)", y = "-log10 P-value (Bambu)")`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'
Warning: Removed 662 rows containing non-finite values (`stat_smooth()`).
logfc <- data.frame(Salmon = both_sorted_res_salmon_0.1$log2fc, Bambu = both_sorted_res_bambu_0.1$log2fc)
ggplot(data = logfc, mapping = aes(x = Salmon, y = Bambu)) +
geom_point() +
geom_smooth() +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
scale_color_viridis() +
labs(title = "Comparison of LogFC (NDR=0.1)", x = "LogFC (Salmon)", y = "LogFC (Bambu)")`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'
Warning: Removed 2 rows containing non-finite values (`stat_smooth()`).
The comparison of the adjusted p-values for transcripts shows low correlation between technologies especially for higher values. The logFC values seem to be, however, better correlated with some deviations for the extreme values.
NDR 0.2
# Transcript to gene mappings
txdf <- df_list_meta$metagenes_0.2
res_salmon_0.2 <- DTU(salmon_0.2, txdf, "salmon_0.2.", n = 3, n.small = 3)
2 3 4 5 6 7 8 9
5393 3052 1297 467 115 31 6 3
converting counts to integer mode
Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors
28 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT
[1] 1578
[1] 2569
The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.
groupID featureID featureID.1 groupID.1
318 ENSG00000064313 ENST00000378164 ENST00000378164.7 ENSG00000064313.13
319 ENSG00000064313 ENST00000686879 ENST00000686879.1 ENSG00000064313.13
4464 ENSG00000198838 ENST00000389232 ENST00000389232.9 ENSG00000198838.14
4465 ENSG00000198838 ENST00000415757 ENST00000415757.7 ENSG00000198838.14
4466 ENSG00000198838 ENST00000634418 ENST00000634418.1 ENSG00000198838.14
4467 ENSG00000198838 ENST00000634730 ENST00000634730.1 ENSG00000198838.14
gene transcript
318 0.04985152 0
319 0.04985152 0
4464 0.04982910 1
4465 0.04982910 1
4466 0.04982910 1
4467 0.04982910 1
gid tid day0.rep1 day0.rep2 day0.rep3
13929 ENSG00000010671.17 ENST00000308731.8 0.00000 0.00000 0.00000
13930 ENSG00000010671.17 ENST00000621635.4 34.28343 18.35999 21.86282
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
13929 3.846644 62.47691 913.4393 848.918664 2209.66400 2287.05736 1190.06724
13930 33.658133 0.00000 0.0000 8.475062 57.90694 28.53335 46.65431
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
13929 1114.41512 34.28343 18.35999 21.86282 33.658133 0.00000
13930 41.67596 0.00000 0.00000 0.00000 3.846644 62.47691
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
13929 0.0000 8.475062 57.90694 28.53335
13930 913.4393 848.918664 2209.66400 2287.05736
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.283430
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.359993
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.862819
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.846644
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.658133
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.476905
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 913.439336
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 848.918664
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.475062
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.906943
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2209.664002
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2287.057357
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.533345
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.654307
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1190.067244
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.415121
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.675958
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.283430
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.359993
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.862819
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.846644
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.658133
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.476905
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 913.439336
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 848.918664
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.475062
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.906943
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2209.664002
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2287.057357
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.533345
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.654307
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1190.067244
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.415121
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.675958
gid tid day0.rep1 day0.rep2 day0.rep3
13929 ENSG00000010671.17 ENST00000308731.8 0.00000 0.00000 0.00000
13930 ENSG00000010671.17 ENST00000621635.4 34.28343 18.35999 21.86282
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
13929 3.846644 62.47691 913.4393 848.918664 2209.66400 2287.05736 1190.06724
13930 33.658133 0.00000 0.0000 8.475062 57.90694 28.53335 46.65431
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
13929 1114.41512 34.28343 18.35999 21.86282 33.658133 0.00000
13930 41.67596 0.00000 0.00000 0.00000 3.846644 62.47691
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
13929 0.0000 8.475062 57.90694 28.53335
13930 913.4393 848.918664 2209.66400 2287.05736
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.283430
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.359993
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.862819
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.846644
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.658133
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.476905
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 913.439336
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 848.918664
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.475062
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.906943
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2209.664002
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2287.057357
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.533345
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.654307
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1190.067244
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.415121
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.675958
sample_id day gid tid value
1 day0.rep1 0 ENSG00000010671.17 ENST00000621635.4 34.283430
2 day0.rep1 0 ENSG00000010671.17 ENST00000308731.8 0.000000
3 day0.rep2 0 ENSG00000010671.17 ENST00000308731.8 0.000000
4 day0.rep2 0 ENSG00000010671.17 ENST00000621635.4 18.359993
5 day0.rep3 0 ENSG00000010671.17 ENST00000308731.8 0.000000
6 day0.rep3 0 ENSG00000010671.17 ENST00000621635.4 21.862819
7 day1.rep1 1 ENSG00000010671.17 ENST00000308731.8 3.846644
8 day1.rep1 1 ENSG00000010671.17 ENST00000621635.4 33.658133
9 day2.rep1 2 ENSG00000010671.17 ENST00000308731.8 62.476905
10 day2.rep1 2 ENSG00000010671.17 ENST00000621635.4 0.000000
11 day3.rep1 3 ENSG00000010671.17 ENST00000308731.8 913.439336
12 day3.rep1 3 ENSG00000010671.17 ENST00000621635.4 0.000000
13 day3.rep2 3 ENSG00000010671.17 ENST00000308731.8 848.918664
14 day3.rep2 3 ENSG00000010671.17 ENST00000621635.4 8.475062
15 day4.rep1 4 ENSG00000010671.17 ENST00000621635.4 57.906943
16 day4.rep1 4 ENSG00000010671.17 ENST00000308731.8 2209.664002
17 day5.rep1 5 ENSG00000010671.17 ENST00000308731.8 2287.057357
18 day5.rep1 5 ENSG00000010671.17 ENST00000621635.4 28.533345
19 day5.rep2 5 ENSG00000010671.17 ENST00000621635.4 46.654307
20 day5.rep2 5 ENSG00000010671.17 ENST00000308731.8 1190.067244
21 day5.rep3 5 ENSG00000010671.17 ENST00000308731.8 1114.415121
22 day5.rep3 5 ENSG00000010671.17 ENST00000621635.4 41.675958
2 3 4 5 6 7 8
4966 1960 673 191 45 9 3
converting counts to integer mode
Warning in DESeqDataSet(rse, design, ignoreRank = TRUE): some variables in
design formula are characters, converting to factors
11 rows did not converge in beta, labelled in mcols(object)$fullBetaConv. Use larger maxit argument with nbinomLRT
[1] 3530
[1] 7799
The returned adjusted p-values are based on a stage-wise testing approach and are only valid for the provided target OFDR level of 5%. If a different target OFDR level is of interest,the entire adjustment should be re-run.
groupID featureID featureID.1 groupID.1
5737 ENSG00000162614 ENST00000330010 ENST00000330010.12 ENSG00000162614.19
5738 ENSG00000162614 ENST00000334785 ENST00000334785.12 ENSG00000162614.19
5739 ENSG00000162614 ENST00000401035 ENST00000401035.7 ENSG00000162614.19
8363 ENSG00000198774 BambuTx2106 BambuTx2106 ENSG00000198774.5
8364 ENSG00000198774 ENST00000361228 ENST00000361228.5 ENSG00000198774.5
7218 ENSG00000180879 BambuTx3324 BambuTx3324 ENSG00000180879.14
gene transcript
5737 0.04987062 0.01990172
5738 0.04987062 0.71463240
5739 0.04987062 0.66990944
8363 0.04986906 0.00000000
8364 0.04986906 0.00000000
7218 0.04982645 0.00000000
gid tid day0.rep1 day0.rep2 day0.rep3
7024 ENSG00000004864.14 ENST00000265631.10 2346.627 1944.294 2181.709
7025 ENSG00000004864.14 ENST00000416240.6 2940.430 2123.040 2312.630
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
7024 2009.438 3398.837 2367.424 2374.237 1881.663 0.000 0.000
7025 2696.543 3398.837 2561.099 2374.237 1881.663 3190.367 3430.594
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
7024 0.000 2940.430 2123.040 2312.630 2696.543 3398.837
7025 2955.513 2346.627 1944.294 2181.709 2009.438 3398.837
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
7024 2561.099 2374.237 1881.663 3190.367
7025 2367.424 2374.237 1881.663 0.000
sample_id day gid tid value
1 day0.rep1 0 ENSG00000004864.14 ENST00000416240.6 2940.430
2 day0.rep1 0 ENSG00000004864.14 ENST00000265631.10 2346.627
3 day0.rep2 0 ENSG00000004864.14 ENST00000265631.10 1944.294
4 day0.rep2 0 ENSG00000004864.14 ENST00000416240.6 2123.040
5 day0.rep3 0 ENSG00000004864.14 ENST00000265631.10 2181.709
6 day0.rep3 0 ENSG00000004864.14 ENST00000416240.6 2312.630
7 day1.rep1 1 ENSG00000004864.14 ENST00000265631.10 2009.438
8 day1.rep1 1 ENSG00000004864.14 ENST00000416240.6 2696.543
9 day2.rep1 2 ENSG00000004864.14 ENST00000265631.10 3398.837
10 day2.rep1 2 ENSG00000004864.14 ENST00000416240.6 3398.837
11 day3.rep1 3 ENSG00000004864.14 ENST00000265631.10 2367.424
12 day3.rep1 3 ENSG00000004864.14 ENST00000416240.6 2561.099
13 day3.rep2 3 ENSG00000004864.14 ENST00000265631.10 2374.237
14 day3.rep2 3 ENSG00000004864.14 ENST00000416240.6 2374.237
15 day4.rep1 4 ENSG00000004864.14 ENST00000416240.6 1881.663
16 day4.rep1 4 ENSG00000004864.14 ENST00000265631.10 1881.663
17 day5.rep1 5 ENSG00000004864.14 ENST00000265631.10 0.000
18 day5.rep1 5 ENSG00000004864.14 ENST00000416240.6 3190.367
19 day5.rep2 5 ENSG00000004864.14 ENST00000416240.6 3430.594
20 day5.rep2 5 ENSG00000004864.14 ENST00000265631.10 0.000
21 day5.rep3 5 ENSG00000004864.14 ENST00000265631.10 0.000
22 day5.rep3 5 ENSG00000004864.14 ENST00000416240.6 2955.513
sample_id day gid tid value
1 day0.rep1 0 ENSG00000004864.14 ENST00000416240.6 2940.430
2 day0.rep1 0 ENSG00000004864.14 ENST00000265631.10 2346.627
3 day0.rep2 0 ENSG00000004864.14 ENST00000265631.10 1944.294
4 day0.rep2 0 ENSG00000004864.14 ENST00000416240.6 2123.040
5 day0.rep3 0 ENSG00000004864.14 ENST00000265631.10 2181.709
6 day0.rep3 0 ENSG00000004864.14 ENST00000416240.6 2312.630
7 day1.rep1 1 ENSG00000004864.14 ENST00000265631.10 2009.438
8 day1.rep1 1 ENSG00000004864.14 ENST00000416240.6 2696.543
9 day2.rep1 2 ENSG00000004864.14 ENST00000265631.10 3398.837
10 day2.rep1 2 ENSG00000004864.14 ENST00000416240.6 3398.837
11 day3.rep1 3 ENSG00000004864.14 ENST00000265631.10 2367.424
12 day3.rep1 3 ENSG00000004864.14 ENST00000416240.6 2561.099
13 day3.rep2 3 ENSG00000004864.14 ENST00000265631.10 2374.237
14 day3.rep2 3 ENSG00000004864.14 ENST00000416240.6 2374.237
15 day4.rep1 4 ENSG00000004864.14 ENST00000416240.6 1881.663
16 day4.rep1 4 ENSG00000004864.14 ENST00000265631.10 1881.663
17 day5.rep1 5 ENSG00000004864.14 ENST00000265631.10 0.000
18 day5.rep1 5 ENSG00000004864.14 ENST00000416240.6 3190.367
19 day5.rep2 5 ENSG00000004864.14 ENST00000416240.6 3430.594
20 day5.rep2 5 ENSG00000004864.14 ENST00000265631.10 0.000
21 day5.rep3 5 ENSG00000004864.14 ENST00000265631.10 0.000
22 day5.rep3 5 ENSG00000004864.14 ENST00000416240.6 2955.513
gid tid day0.rep1 day0.rep2 day0.rep3
7024 ENSG00000004864.14 ENST00000265631.10 2346.627 1944.294 2181.709
7025 ENSG00000004864.14 ENST00000416240.6 2940.430 2123.040 2312.630
day1.rep1 day2.rep1 day3.rep1 day3.rep2 day4.rep1 day5.rep1 day5.rep2
7024 2009.438 3398.837 2367.424 2374.237 1881.663 0.000 0.000
7025 2696.543 3398.837 2561.099 2374.237 1881.663 3190.367 3430.594
day5.rep3 day0.rep1.1 day0.rep2.1 day0.rep3.1 day1.rep1.1 day2.rep1.1
7024 0.000 2940.430 2123.040 2312.630 2696.543 3398.837
7025 2955.513 2346.627 1944.294 2181.709 2009.438 3398.837
day3.rep1.1 day3.rep2.1 day4.rep1.1 day5.rep1.1
7024 2561.099 2374.237 1881.663 3190.367
7025 2367.424 2374.237 1881.663 0.000
sample_id day gid tid value
1 day0.rep1 0 ENSG00000004864.14 ENST00000416240.6 2940.430
2 day0.rep1 0 ENSG00000004864.14 ENST00000265631.10 2346.627
3 day0.rep2 0 ENSG00000004864.14 ENST00000265631.10 1944.294
4 day0.rep2 0 ENSG00000004864.14 ENST00000416240.6 2123.040
5 day0.rep3 0 ENSG00000004864.14 ENST00000265631.10 2181.709
6 day0.rep3 0 ENSG00000004864.14 ENST00000416240.6 2312.630
7 day1.rep1 1 ENSG00000004864.14 ENST00000265631.10 2009.438
8 day1.rep1 1 ENSG00000004864.14 ENST00000416240.6 2696.543
9 day2.rep1 2 ENSG00000004864.14 ENST00000265631.10 3398.837
10 day2.rep1 2 ENSG00000004864.14 ENST00000416240.6 3398.837
11 day3.rep1 3 ENSG00000004864.14 ENST00000265631.10 2367.424
12 day3.rep1 3 ENSG00000004864.14 ENST00000416240.6 2561.099
13 day3.rep2 3 ENSG00000004864.14 ENST00000265631.10 2374.237
14 day3.rep2 3 ENSG00000004864.14 ENST00000416240.6 2374.237
15 day4.rep1 4 ENSG00000004864.14 ENST00000416240.6 1881.663
16 day4.rep1 4 ENSG00000004864.14 ENST00000265631.10 1881.663
17 day5.rep1 5 ENSG00000004864.14 ENST00000265631.10 0.000
18 day5.rep1 5 ENSG00000004864.14 ENST00000416240.6 3190.367
19 day5.rep2 5 ENSG00000004864.14 ENST00000416240.6 3430.594
20 day5.rep2 5 ENSG00000004864.14 ENST00000265631.10 0.000
21 day5.rep3 5 ENSG00000004864.14 ENST00000265631.10 0.000
22 day5.rep3 5 ENSG00000004864.14 ENST00000416240.6 2955.513
sample_id day gid tid value
1 day0.rep1 0 ENSG00000004864.14 ENST00000416240.6 2940.430
2 day0.rep1 0 ENSG00000004864.14 ENST00000265631.10 2346.627
3 day0.rep2 0 ENSG00000004864.14 ENST00000265631.10 1944.294
4 day0.rep2 0 ENSG00000004864.14 ENST00000416240.6 2123.040
5 day0.rep3 0 ENSG00000004864.14 ENST00000265631.10 2181.709
6 day0.rep3 0 ENSG00000004864.14 ENST00000416240.6 2312.630
7 day1.rep1 1 ENSG00000004864.14 ENST00000265631.10 2009.438
8 day1.rep1 1 ENSG00000004864.14 ENST00000416240.6 2696.543
9 day2.rep1 2 ENSG00000004864.14 ENST00000265631.10 3398.837
10 day2.rep1 2 ENSG00000004864.14 ENST00000416240.6 3398.837
11 day3.rep1 3 ENSG00000004864.14 ENST00000265631.10 2367.424
12 day3.rep1 3 ENSG00000004864.14 ENST00000416240.6 2561.099
13 day3.rep2 3 ENSG00000004864.14 ENST00000265631.10 2374.237
14 day3.rep2 3 ENSG00000004864.14 ENST00000416240.6 2374.237
15 day4.rep1 4 ENSG00000004864.14 ENST00000416240.6 1881.663
16 day4.rep1 4 ENSG00000004864.14 ENST00000265631.10 1881.663
17 day5.rep1 5 ENSG00000004864.14 ENST00000265631.10 0.000
18 day5.rep1 5 ENSG00000004864.14 ENST00000416240.6 3190.367
19 day5.rep2 5 ENSG00000004864.14 ENST00000416240.6 3430.594
20 day5.rep2 5 ENSG00000004864.14 ENST00000265631.10 0.000
21 day5.rep3 5 ENSG00000004864.14 ENST00000265631.10 0.000
22 day5.rep3 5 ENSG00000004864.14 ENST00000416240.6 2955.513
confirmed_salmon_0.2 <- res_salmon_0.1[res_salmon_0.2$transcript < 0.05, ]
nrow(confirmed_salmon_0.2)[1] 2528
[1] 7108
For Illumina+Salmon, out of the 10364 tested genes and 28447 tested features, DEXSeq test identified 1578 genes showing evidence of isoform switching involving 2569 transcripts. For PacBio+Bambu out of the 7847 tested genes and 19816 tested features, 3530 genes involving 7799 trancsripts were identified.
After the stageR procedure, 2528 transcripts passed the confirmation stage for Illumina+Salmon and 7108 transcripts for PacBio+Bambu on a target 5% overall false discovery rate (OFDR). This means that, in expectation, no more than 5% of the genes that pass screening will either (1) not contain any DTU, so be falsely screened genes, or (2) contain a falsely confirmed transcript.
Upset Plot
[1] 697
# Confirmed Transcripts
length(intersect(confirmed_salmon_0.2$TranscriptID, confirmed_bambu_0.2$TranscriptID))[1] 654
venn <- list(SALMON = confirmed_salmon_0.2$TranscriptID, BAMBU = confirmed_bambu_0.2$TranscriptID)
ggvenn(venn)From the UpSet plot and Venn Diagram above it is visible that through PacBio+Bambu many more transcripts were detected through DTU. The overlap between Illumina+Salmon was also only roughly 7 %. This percentage is much less than for the cutoffs from before.
Comparsion of pAdj and logFC
both_detected <-
intersect(res_bambu_0.2$TranscriptID, res_salmon_0.2$TranscriptID)
sorted_res_salmon_0.2 <- res_salmon_0.2[order(res_salmon_0.2$TranscriptID),]
both_sorted_res_salmon_0.2 <- sorted_res_salmon_0.2[which(sorted_res_salmon_0.2$TranscriptID %in% both_detected), ]
sorted_res_bambu_0.2 <- res_bambu_0.2[order(res_bambu_0.2$TranscriptID),]
both_sorted_res_bambu_0.2 <- sorted_res_bambu_0.2[which(sorted_res_bambu_0.2$TranscriptID %in% both_detected), ]
padj <- data.frame(Salmon = both_sorted_res_salmon_0.2$transcript, Bambu = both_sorted_res_bambu_0.2$transcript)
ggplot(data = padj, mapping = aes(x = -log10(Salmon), y = -log10(Bambu))) +
geom_point() +
geom_smooth() +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
scale_color_viridis() +
labs(title = "Comparison of P-values (NDR=0.2)", x = "-log10 P-value (Salmon)", y = "-log10 P-value (Bambu)")`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'
Warning: Removed 674 rows containing non-finite values (`stat_smooth()`).
logfc <- data.frame(Salmon = both_sorted_res_salmon_0.2$log2fc, Bambu = both_sorted_res_bambu_0.2$log2fc)
ggplot(data = logfc, mapping = aes(x = Salmon, y = Bambu)) +
geom_point() +
geom_smooth() +
theme_minimal() +
theme(plot.title = element_text(hjust = 0.5)) +
scale_color_viridis() +
labs(title = "Comparison of LogFC (NDR=0.2)", x = "LogFC (Salmon)", y = "LogFC (Bambu)")`geom_smooth()` using method = 'gam' and formula = 'y ~ s(x, bs = "cs")'
The comparison of the adjusted p-values for transcripts shows low correlation between technologies especially for higher values. The logFC values seem to be, however, better correlated with some deviations for the extreme values.